As per Hindu legend, the sage Bharadwaja worshipped the presiding deity in the form of a sparrow named Valiyan. The place was hence called Valithayam, meaning the one worshipped by a sparrow.
Padi historically is referred to the place used to store armory.
The God here is worshipped by Ramar, Bharathwajar, Anjaneyar, Surya, Chandra, Indran and Valiyan. During the medieval times, the place was the site for multiple wars, which raged the structure of the temple.
As per Tamil mention, the resting place near a war field is called Padi, which lead to the modern name of the place
As per another legend, Planet Jupiter who was cursed by Menaka.
On the advice of Markendeya, he reached this place, got a dip and worshipped the presiding deity and got relief from the curse. Devotees pray to the Jupiter to get remedy for their relief from sins.
The historic name of the place is Thiruvalidayil, which went on to become Thiruvalithayam.
The original structure of the temple is believed to have been built by The temple is closely associated with Rajaraja Chola III. There are 14 inscriptions from the Chola empire, with the oldest dating back to Tribuvana Chakravarthy Vijayakanda Gopalan who donated multiple jewels to Nachiyar.
The inscriptions are counted as 214-28 of 1910. As per the inscriptions, during the regime of Rajaraja III, the temple was in a place called Chintamanipuram. The temple is referred as Ambattur Nadu, Puzhar kottam and Jayamkonda Cholapuram in various inscriptions.
The inscriptions denote the presiding deity as Thiruvalithamudaya Nayanar and the Ambal as Thiruveethi Nachiyar.
During the period of Rajaraja, a devotee named Chalukya Naranan Yathavarayan donated two houses and two gardens to the temple. The other inscriptions indicate gifts in the form of lamps, food and gold to the temple by various devotees and ruling kings.