The temple is constructed in Dravidian style of architecture. It is classified as Gnazhar Kovil, where the image of the presiding deity is set up under Gnazhar trees. Trees like Kondai, Kongu and Theekku (teak) all fall in the category. The temples constructed in wood made from Gnazhar trees are also classified as Gnzhar Koil. Literary evidence is found in the works of Tirugnanasambandar, who refers the temple as Gnazhar Koil.
Appar's sister Thilakavathiyar was living in Thiruvathigai during her later years and devoted her lifetime service to Shiva. Afflicted by a painful illness, Thirunavukkarasar, who was originally called Dharmasenar and was then a staunch follower of Jainism, prayed for relief at this temple where his sister Thilagavathiyar served. By the divine grace of Shiva, he was cured. He embraced Saivism from then and started canonizing various temples with his verses.
The ruling Pallava king namely Kadava punished Thirunavukarasar in various ways and finally dropped him in a lime kiln. He was subsequently cast on the waters of sea, where he started floating and was pushed ashore in Thirupathipuliyur. It is believed that some of his best songs were sung at this time in praise of the presiding deities at Padaleeswarar temple and Veerateneeswarar temple. Influenced by the greatness of the poet, the king himself converted from Jainism to Saivism.