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Once, there was an argument in Brahma Lok between Saraswathi and Lakshmi  that who is greatest among the two. Brahma said that it  is  Lakshmi Thaayar who is found on the heart of Sri Vishnu is the greatest. 

Next, Saraswathi asked which river is the biggest river. But, unfortunately Brahma answered that the greatest river is River Ganga, which is originating from the feet of Sri Vishnu. 

On hearing this, Saraswathi got angry, disappeared and went  to the bank of river Ganga and started doing Tapas.

Brahma wanted to do the great Ashwametha Yagam in Kanchipuram and wanted Saraswathi to be along with Him. So, He sent His son Vashista to bring Saraswathi  to  Kanchipuram. But, Saraswathi refused to come along with him. After this, Brahma started the Yagam.

On seeing this, the demons wanted to destroy the Yagam, went to Saraswathi and made Her angry by narrating about the yagam. She got angry on Brahma  and started as "Vegavathi" river along the south direction and flow across the place of the Yagam to destroy it . 

But, Sriman Narayanan wanted to stop Vegavathi river and protect the Yagam from her. So, He stopped the river by lying across the river on Aadhiseshan. Because of this, the Perumal is also named as "Vaga Sethu". The place came to be known as  Vega Anai, Vakkanai or Thiru Vekka.

The Moolavar of this sthalam is Sri Yathothakaari. Other names are Sonnavannam seitha Perumal and Vegasethu. Moolavar is Kidantha Kolam (Bhujanga Sayanam), facing in West direction. 

This perumal is found in Sleeping posture from right side to left. This is also one of the specialty of this  temple. Lord Vishnu, here at ThiruVekka, is seen in a different sleeping posture from right to left (Maaru Sayanam) with His head resting on the left hand. In all other Divya Desams, where the Lord is represented in a sleeping posture, He can be seen sleeping from left to right with His head resting on His right hand.

The legend has that Thirumazhisai Alwar, lived in Kanchi and served Lord Yathothkari Perumal in this temple. There was a Dasi woman, who used to clean the temple premises and in this way she selflessly served the Lord. 

Seeing her sincerity and self-less devotion to Lord, Thirumazhisai  Alwar blessed her to become a beautiful maiden. Later, the King of this city fell in love over the enchanting beautify of this lady and married her.

The King learned the truth of her captivating attractiveness and decided to meet Thirumazhisai  Alwar.

Kanikannan was a close associate and an ardent follower of Thirumazhisai Alwar. One day, the King ordered Kanikannan to appear before the court.

Kanikannan was produced before the assembly. The King demanded Kanikannan to bring Thirumazhisai  Alwar to the palace so that he could listen to Alwar singing and praising the glories of him. 

Kanikannan  revealed the fact that Thirumazhisai Alwar sung praising the glories of no one other than Lord Vishnu and it would be an impossible task for him to sing praising the King.

Then, the King persuaded Kanikannan with all the precious jewels, diamonds, etc. to praise his virtues. Kanikannan flatly refused to do so. The King was totally annoyed at the arrogant act of Kanikannan and ordered him to stay out of Kanchi as soon as possible.

Kanikannan explained to Thirumazhisai Alwar about the whole incident that happened at the assembly of the King and his final verdict to leave the city. He prepared to leave Kanchi to follow the verdict. Soon, Thirumazhisai Alwar also decided to  join him and leave the city. 

Before leaving this temple, Thirumazhisai Alwar fervently sung beautiful verses requesting Lord to be with them on their way out of Kanchi. Lord Yathothkari Perumal also decided to leave Kanchi  admiring the true passion of Thirumazhisai  Alwar. 

Shortly, the King realized the absence of Lord in the temple and deeply regretted at his ignorance. He requested Kanikannan to pardon him and received Kanikannan and his Acharya with due respect and honor to Kanchi.

When returning, Alwar sung a song asking that Kani Kannan has returned back to Kanchi and he wanted the Perumal to go and sleep on His Aadhiseshan in the temple. On hearing this, Sriman Narayanan came back to Thiruvekka temple and gave His sayana kola seva. 

Since the Perumal obeyed the words of Thirumizhisai Alwar and did what he said, He is called as “Sonna Vannam seitha perumal”. Earlier, He did according to the wishes of Brahma; and then as told by Tirumazhisai Alwar; in future, He might do as we pray to Him!

The central shrine of the temple has the image of presiding deity, "Sonnavannam Seitha Perumal" sported in Bhuganja Sayanam posture. The West facing sanctum is approached through the flagstaff, pillared halls, namely Mahamandapam and the Ardhamandapam. The stucco image of the presiding deity is a rare one of Ranganatha recumbent on his left hand unlike other temples where he is recumbent on his right. It is believed that Perumal was lying left to right as in other temples, but on hearing Thirumalisai Azhwar sing, he turned his lying posture from right to left. As per historian Nagaswamy, the image made of stucco, is one of the rarest representation of the deity. The image of Saraswathi praying at his feet is also present in the sanctum. The roof of the sanctum is called Vedasara Vimana and it has five kalasams and stucco images of various legend. The temple has separate shrines for Poigai Azhwar located to the North of the flagstaff. There are other shrines of Rama along with Seetha and Hanuman and Garuda. The vimana of the central shrine is called Vedasara Vimana. The shrine of Komavalli, the consort of Yathothkari, is located facing the central shrine in the Eastern side of the temple. The temple lotus tank where Poigai Azhwar was born is located outside the main entrance, parallel to the shrine. The Mahamandapa has ornamental sculpted pillars built during the Vijayanagara period of 15-16th centuries The temple has two precincts with the second precinct enclosed by granite walls pierced by a five tiered rajagopuram (gateway tower).