The place got the name of Suchindrum from the Sthala Purana. Hindu mythological legend has it that king of devas, Indra got relieved of a curse at the place of the main linga in the temple. The term "Suchi" in Suchindrum is believed to have derived from the Sanskrit meaning that stands for "purify". Accordingly, Indra is supposed to visit the temple for performing "Ardhajama Pooja", or worship, at midnight every day.
As per another legend, sage Atri and his wife Anasuya stayed at Jnaranya. Sage Anasuya was highly devoted to her husband. The trinity of Hinduism, namely, Shiva, Vishnu and Brahma wanted to make her name eternal with their divine act. They came to the sage's hermitage as Brahmin mendicants. Anasuya treated them with utmost care. The Brahmins put forth a condition that they would accept her hospitality with a condition that she would come out nude.
With her power of chastity, she converted the three to small kids and served them with her breast milk. Atri returned to the hermitage at the behest of Parvathi, Saraswathi and Lakshmi (the wives of the trinity) to restore their husbands to their original form. Anasuya obliged immediately and restored the kids to their original form. The trinity blessed the couple for their devotion. The three emanated in the form of three Lingas and the place where the couple worshiped the trinity is believed to be the temple.
There are several inscriptions from the period of early and medieval Cholas along with other Pandya rulers and Chera rulersin the region. There are two records from Kopparakesarivarman who took Madurai and Eezham (Sri lanka) from the 30th and 40th regnal year of Parantaka I (907-950 CE).The current temple was renovated in the 17th century and is famous for its sculptures.
It was previously administered and controlled by "Thekkumon Madam", a famous namboothiri priest family. The main deity of the temple is Lord Shiva, Lord Vishnu and Lord Brahma in a single form called Sthanumalyam. This 17th-century temple is famous for its architectural grandeur. The seven-storey white gopuram (gateway tower) is visible from the distance. Its 40 m (130 ft) facade is covered with sculptures of Hindu deities.
Thirumalai Nayak and the Travancore Maharajas, under whose administration the temple remained till Kanyakumari's merger with Tamil Nadu, have made many endowments for its upkeep. During the reign of Ayilyam Thirunal Rama Varma Maharajah of Travancore, a lottery scheme was introduced in 1875 A.D., to raise funds for rebuilding a portion of the temple and a sum of over Rs. 40,000 was realised.