
The floor of the temple complex is stone-layed and there is no permanent flagpole. The temple pond can be seen on the north-eastern side of the temple. On the southern side of the Eastern entrance, Hanuman's idol is consecrated. The idol is nearly five feet tall. The uniqueness of Vilwadrinatha temple is that one could see two main shrines inside the Nalambalam, which are considered equally important. The idol inside the shrine which faces west is believed to be of Sri Rama. It is said that this shrine will be the topper of the five major Sri Rama shrines in Kerala. Other important ones are Kadavalloor, Thriprayar, Thiruvangadu etc. The idol consecrated inside the eastern shrine is said to be of Lakshmana. The roofs of both shrines of Thiruvilwamala are covered with copper. Usually, devotees circumvent both shrines together. It is believed that for those who pray at the western shrine first will get salvation after the death while for those who worship at the eastern shrine first will be blessed with earthly pleasures.

The idol on the western shrine (of Sri Rama aka Vilwadrinathan) is approximately five feet tall. The idol is having four hands with discus, conch, lotus and club in them. Hence devotees also worship the idol as Lord Vishnu himself (Sri Rama is said to be the seventh incarnation of Lord Vishnu). This self-manifested stone (Anjanashila) idol is completely covered with golden plates. On either side of the idol of Vilwadrinathan, there are idols of Lakshmi Devi and Bhoomi Devi, the consorts of Lord Vishnu. One could see three rooms in front of the Garbhagriha and there is no Mughamandapam in front of the shrine.
It is believed that there exists a large cave beneath the temple where grows a golden Vilwa tree and hence this place is called as Thiruvilwamala. It is also said that Vilwamangalam Swamiyar was the first one to praise the deity by the name Vilwadrinathan.
The idol on the eastern shrine is identical to the one in the west. Here also the idol possesses four hands but is worshipped as Lakshmana and is approximately three feet tall. It is believed that this shrine was built first. The temples of Lakshmana are very rare in Kerala. Thiruvilwamala and Vennimala are the most celebrated Lakshmana shrines in Kerala. Another feature of the temple is that both shrines are having seperate Tantris and Melshantis(chief priests). Both shrines are rectangular in shape. There are no carvings or murals on the walls of both the shrines. On the southern side of the srikovil there is a shrine of Lord Ganapathy. The temple is at present administered by the Cochin Devaswom Board.
While circumambulating the temple, as a custom one should also pray Vadakumanathan, Navamukundan, Pazhani Murugan and Guruvayoorappan when reaching at certain locations.
Outside the temple and down below on the southern side, a flight of stone steps lead to the shrine of Lord Ayyappa installed on the same pedestal as Shiva and Parvati.

'Sri Vilwadri Mahatmyam', a Sanskrit text with 18 chapters, describes the origin of this ancient temple. It is in the form of a conversation between Parvati and Shiva. According to legend, the eastern idol (of Lakshmana) was installed by Parasurama. Parasurama prayed to Shiva to save the spirits of Kshatriyas which he had killed in the battle and to help them to attain salvation. Pleased with the implorations of Parasurama, Shiva granted him the image of Lord Vishnu, which he himself was worshipping. Parasurama, in his search for a suitable place for the installation of the deity, came across the bewitching Vilwadri, full of Amala trees. He constructed a temple here, consecrated the deity and laid down the pooja routine.
The story of the origin of western idolis also related in the 'Sri Vilwadri Mahatmyam'. According to this, Sage Aamalaka, the son of Kashyapa Prajapati, started a rigorous meditation to propitiate Lord Mahavishnu. Indra thought his objective was to conquer heaven. He, therefore, deputed the celestial beauties like Urvasi, Rambha, Tilothama etc. to interrupt the meditation. But all these celestial epitomes of beauty failed miserably in their venture. Kashyapa himself explained to Indra that Aamalaka had no ambition to conquer heaven nor was
he interested in things which are transient. He was only interested in attaining unstinted devotion to Lord Vishnu.
Then the Asuras became horrified as they thought that this severe penance would bring about their destruction. They decided to make an end to it and tried to disrupt his penance physically. But the latter opened his eyes, which emitted sparks, which ultimately turned into a huge fire. The asuras became breathless and died on the very spot. The heap of the corpuses was transformed into rock, which is even now known as 'Rakshasapara' to the south east of the present temple.
Sage Aamalaka continued his prayer and pleased by his perseverance, four-armed Lord Mahavishnu accompanied by Lakshmi devi and Bhoomi devi appeared before him. The sage shed tears of joy and bowed before the omnipotent Lord.
When Mahavishnu told the sage to ask for a boon, Aamalaka said that he desired nothing in this world, not even heaven and what he wanted was only pure and focussed devotion on Lord Vishnu. He also requested the Lord to remain there for the protection of those who suffer with worldly troubles. Hence Lord Vishnu manifested there as a swayambhoo idol. Aamalaka Maharshi used to chant Sri Rama's names while doing penance, hence people worshipped the deity on the western shrine as Sri Rama. Consequently the idol on the east side came to be regarded as Lakshmana, Rama's brother.
About 3 Kms from the temple on the east side, there is a cave in the south-west direction. This is called 'Punarjani' and is believed to have been built by Viswakarma, the celestial builder at the behest of Parasurama. Unless human beings complete the proscribed number of births and deaths, they cannot attain salvation. It is as a result of deeds that man takes birth, again and again. Passing through this cave once is believed to relieve devotee of one such birth.

The story goes that it was Parasurama who brought the Ganges to Kerala, which is known as Bharatapuzha. Just as the Ganga has several bathing ghats with each having a Shiva temple, on the banks of Bharatapuzha there are five holy places, namely Tiruvilwamala, Tirunjikuzhi, Trithala, Tirunavaya, and Thirumittakodu with Vishnu-shiva temples on either side.
The important annual festival here is Ekadasi which falls in the Malayalam month of Kumbham (February- March).
This temple, along with several other Kerala temples, was attacked by Tipu Sultan. It was also destroyed by repeated fires. In 1789 AD, Tipu's army attacked the temple and almost destroyed it. But when they heard that the temple belonged to Cochin Kingdom with whom Tipu Sultan had good relations, abandoned further attack and the sanctum was thus saved.
The Government of Cochin renovated the entire temple. The work was completed in 1861 AD and a date for purificatory rites was fixed. But sadly, the same night a fire broke out. The idol on the eastern shrine was plucked out and is taken near the temple tank and was saved. The image on the western shrine could not be removed for being swayambhoo. It took 25 days for the embers to die out and when the idol on the western shrine was examined thereafter, surprisingly, it was quite intact. The flames couldn't even make a mark on the idol. The rituals were resumed. The present temple we see is the one renovated by the, erstwhile Cochin Government in 1885 AD.
Parashurama had entrusted the property of the temple and its administration to six illams. They were called Parasudayavar. They belonged to the Moosath caste. The eldest of the six administered the temple in consultation with others. Parasurama also appointed separate Tantris for east and west sanctums, and Namboothiris of five illams as temple priests.
In course of time, the administration of the temple passed on to Perumbadappu Swaroopam(Cochin) and Nediyirippu Swaroopam (Zamorin). As there were frequent quarrels between the two, both had to approach the British for mediation. At that time, mighty Sakthan Thampuran ruled Cochin. The British decided in his favor, although, by virtue of several landed properties lying in the region of Malabar, the administration should have properly gone to the Zamorin. Today the temple is under the administrative control of the Cochin Devaswom Board.