Koodal Aḻagar temple covers an area of about 2 acres (0.81 hectares) and has a five-tiered gopuram (gateway tower) raising to a height of 125 ft (38 m). The temple is enclosed in a rectangular enclosure with huge granite walls. The central shrine has an elevated structure and houses the images of the presiding deity, Koodal Aḻagar, in three forms, namely sitting, standing and reclining postures.
The image made of granite is sported in sitting posture and 6 ft (1.8 m) tall. The images of Sridevi and Bhudevi are present in either sides of Koodal Aḻagar. The festival deity is named Vyuga Sundararajar and the image is 4 ft (1.2 m) tall made of panchaloha. The vimana, the shrine over the sanctum is Ashtanga in architecture, which has eight parts, namely, Adhistana (base), three Padas (struct), Prashthana (limb), Griva (leading struct), Shikara (cylindrical holder) and Stupi (top portion).
The outer parts of the vimana has stucco images of sages, Dashavataram, Bhudevi and Varaha, Lakshmi Narasimha, Lakshmi Narayana, and Narayanamoorthy. The vimana is believed to be the work of Vishvakarma, the divine architect. The shadow of the vimana does not fall on the ground. The Ashtanga Vimana is found in Mannar Koil, Ambasamudram, Uthiramerur, Thirukoshtiyur and Cheranmadevi temples. The inner walls of the sanctum has paintings of the Ashtadikpalakas
The shrine of the consort of Koodal Aḻagar, Mathuravalli, is located to the south of the main shrine. There are smaller shrines of Lakshmi Narasimha, Rama, Lakshmi Narayana, and Krishna located close to the sanctum. The shrines of Andal, Narasimha, and Manavala Mamunigal are found in separate shrines around the first precinct.
The shrine of Andal has painting depicting puranic stories and inscriptions detailing devotional literature. The shrines of Garuda, Anjaneya, Ramanuja, Vedanta Desika and Alvars are found in the second precinct. The pillars in the halls leading to the sanctum have small sculptures, in the second precinct. The second floor has a shrine dedicated to Suryanarayana standing along with goddesses
The Teppakulam, the temple tank, is located outside the temple premises. It has a centre hall made of granite.Periyalvar obtained the name as he is believed to be an ardent worshipper of Vishnu. While coming out of Madurai, he was taken out in procession to Srivilliputhur and he got the divine vision of Vishnu at the instance.
He started reciting his composition, Periya Tirumoli, which was compiled in Naalayira Divya Prabhandam by Manavala Mamunigal. Manavala decreed that the verses of Periyalvar starting with Tirupallandu should be the first and last verse while reciting Pradandam in any sacred occasion in Vishnu temples. Ramanuja, a proponent during the 10th century, believes that Tirupallandu originated at Madurai.
Thus Koodal Aḻagar temple finds an indomitable position in Vaishnavite belief. During Mahapralaya, the great disaster, the devotees sought the abode of Vishnu in Madurai. It is believed that Vishnu stood as a bulwark against the impending disaster, giving him the name of the city as Naanmadakoodal or Koodal Nagar ('Koodal' in Tamil is bulwark).
The place is mentioned to be significant during four ages namely, Satya Yuga, Treta Yuga, Dvapara Yuga and Kali Yuga. The temple has Navagrahas, the nine planetary deities, which are otherwise found only in Shiva temples. It indicates the co-existence of Shaivite and Vaishnavite cultures during the medieval period.
Historians are of the opinion that Koodal Aḻagar temple finds mention in Sangam literature (3 century BCE - 3 century CE) in works like Madurai Kanchi by Mangudi Marudan, Paripāṭal, Kaliththokai and Silappatikaram. Madurai Kanchi details the Thiruvonam festival celebrated in the temple. Koodal Aḻagar temple is revered in Nalayira Divya Prabhandam, the 7th–9th century Vaishnava canon, by Periyalvar, Thirumalisai Alvar and Thirumangai Alvar.
The temple is classified as a Divya Desams, one of the 108 Vishnu temples that are mentioned in the book. During the 18th and 19th centuries, the temple finds mention in several works like 108 Tirupathi Anthathi by Divya Kavi Pillai Perumal Aiyangar and Koodal Sthala Purana
Koodal Purana details the origin of Vaigai river flowing through Madurai. It is believed that Vishnu stood up as Trivikrama, with one of his foot rising to the skies and the foot reached Brahmaloka, the abode of Brahma. Brahma was pleased to perform ablution to the raised foot and the water is believed to have emerged as a rivulet called Krithimala. A large number of banana trees sprang up in the place and it came to be known as Kadhalivana, a forest of banana trees.
Satyavrata, a ruler of Madurai was a staunch devotee of Vishnu. It is believed that once Vishnu came out of the river Krithimala as a fish (Matsya avatar, one of the avatars of Vishnu) to teach Vedas to the ruler. From then on, the Pandyas started having fish as the symbol of the kingdom.