The temple is maintained and administered by the Hindu Religious and Endowment Board of the Government of Tamil Nadu.

According to the temple's regional legend, Somukasura, an asura, defeated Brahma, the Hindu god of creation and stole the four Vedas (sacred texts) from him.

Brahma was helpless, and he did severe penance in the banks of Tamiraparani river, seeking favour from Vishnu in the form of Vaikuntanathan.

Taking form of a divine fish called the Matsya avataram, Vishnu killed the Somukasura and restored the Vedas to Brahma.

[3] As per another legend, the image of Vaikunthanatha, over the period of several ages, had no patrons and was left submerged under the earth.

The temple also obtained grant for building and maintenance of a garden from a ruler who defeated the Cheras.

The Pandya ruler Jatavarman Kulasekaran I (1190–1216 CE) also offered a similar grant to the temple.

It is believed that the marks of war and destruction of Pandiyan history by the later nayakkar were visible in the temple during modern times.

There are separate shrines for Vishvaksena (Senai Mudaliyar), Garuda, Krishna as Venugopala, Manavala Mamunigal and Yoga Narasimha.

[5] Thiruvengadamudayan hall, located to the right of the gopuram, houses rare life size sculptures commissioned during the 16th century.

[3] The composite columns of Virabhadra holding sword and horn are found be additions of the Vijayanayagara kings during the early 1500s.

The corridor inside the temple has paintings having the details about the 108 Divya Desam shrines of Vishnu.

[3] Brahmanda Purana one of the eighteen sacred texts of Hinduism and written by Veda Vyasa contains a chapter called Navathirupathi Mahatmeeyam.

Vaikunta Mahatmeeyam is another work in Sanskrit that glorifies the temple and is a part of Tamraparani Sthalapurana available only in palm manuscripts.

[3] The temple is revered in Nalayira Divya Prabandham, the 7th–9th century Vaishnava canon, by Nammalvar.

During the 18th and 19th centuries, the temple finds mention in several works like 108 Tirupathi Anthathi by Divya Kavi Pillai Perumal Aiyangar, Vaikuntha Pillai Tamil, Vaikuntanatha Thalattu, Vaikuntanatha Tiruppanimalai and Srivakiuntam Ammanai.

[9][10][11] The Garuda Sevai utsavam (festival) in the month of Vaikasi (May-Jun) witnesses 9 Garudasevai, a spectacular event in which festival image idols from the Navatirupathi shrines in the area are brought on Garuda vahana (sacred vehicle).

An idol of Nammalvar is also brought here on an Anna Vahanam (palanquin) and his pasurams (verses) dedicated to each of these 9 temples are recited.

The utsavar (festival deity) of Nammalvar is taken in a palanquin to each of the 9 temples, through the paddy fields in the area.

As at other Vishnu temples of Tamil Nadu, the priests belong to the Vaishnavaite community, from the Brahmin class.

The temple rituals are performed four times a day: Kalasanthi at 8:00 a.m., Uchikalam at 12:00 p.m., Sayarakshai at 6:00 p.m., and Ardha Jamam at 8:00 p.m. Each ritual has three steps: alangaram (decoration), neivethanam (food offering) and deepa aradanai (waving of lamps) for both Vaikunthanathar and Vaikunthavalli.