This Temple is well known for the Musical Pillars. Lord Shiva is worshipped by Agastya in a Bamboo Grove and by Rama after having killed Mareecha some nine miles away at Manoor. The Goddess Sculpture is visible in the Lingam while performing Abhishekam.
According to the puranas, both the Gopurams were built by Muluthukanda Rama Pandiyan and the other important parts of the temple were constructed by Nindraseer Nedumaran who reigned in the 7th century A.D. The mani mandapam with its famous musical pillar was built by Nindaraseer Nedumaran in the 7th century A.D. Originally the Nellaiappar and Kanthimathi temples were two independent structures with spaces in between. It was in 1647 A.D. that Thiru Vadamalaiappa Pillaiyan, a great devotee of Siva linked the two temples by building the "Chain mandapam". To the western portion of the chain, mandapam is the flower garden that was set up in 1756 A.D. by Thiruvengadakrishna Mudaliar.
In the centre of the Flower Garden is a square vasantha mandapm with 100 pillars. The Nandi mandapam is said to have been built by Sivanthiappa Nayak in 1654 A.D. The flag stand near the Nandi was set up in 1155 A.D There are a number of stone inscriptions in the temple. The most important of them are those Veerapandiyan who regained about 950 A.D. and those of Rajendran I and Kulothunga chola I. The inscriptions of Maravarma Sundara Pandiyan refer to the Lord as "Woodayar" and "Wodeyanayanar" and the Goddess as "Nachiar". From the inscriptions of Kulasekkara Pandiyan, we learn that he defeated the Chera, Chola and Hoysala kings and built the outer walls of the temple with the war booty. Siva is said to have been worshipped by Agastya in a bamboo grove and by Rama after having killed Mareecha some nine miles away at Manoor. There is also a shrine to Vishnu near the sanctum, signifying the belief that Nellai Govindan (Vishnu) visited Tirunelveli to officiate the divine marriage of Shiva and Kantimathi.
A little to the south of Swami Nellaiappar Gopuram stands the Gopuram of Arultharum Kanthimathi Ambal temple. It was here, where composer Sri Muthuswami Dikshithar composed the carnatic song 'Sri Kanthimatheem' in Hemavathi ragam. Kanthimathi Nellaiyappar Temple is the well-known twin temple dedicated to Goddess Parvathi and Lord Shiva . Covering an area of 14 acres, it is the biggest temple in Tamil Nadu situated in the heart of the city on the banks of river Taamiraparni at a distance of 2kms from the railway station. The temple, believed to be built by the Pandyas in the 13C was entirely remodelled and extended in 17C - 18C. Some of the inscriptions in the temple dates back to 950A.D. The temple is also known as one of the 5 Pancha Sabhas (dance halls) of Nataraja (lord Shiva); the others being at Chidambaram, Madurai, Tiruvalankadu and Kutralam.
Vast in an area, this temple never ceases to surprise visitors for the wealth of detail it has to offer. The Musical Pillars in the Mani Mandapam which produce sound in various pitches when struck, the Somavara Mandapam, the 1000 pillared hall, and the Tamra sabha with intricate woodwork, and the Vasantha Mandapam are some of the noteworthy points in this temple. Lifelike sculptures adorn several of the Mandapams in the temple, noteworthy ones being in the Sangili Mandapam which links the temples of Nellaiappar and Kantimathi in this vast temple complex.