The temple occupies an area of about 25acres with four large 'gopuram' on each side. The largest 'gopuram' is above the eastern entrance which is the main entrance. There are five 'praharam' or corridors around the central structure with a high wall running on all four sides at the edge of the outer 'praharam'. There are numerous shrines for other deities in the temple complex and Goddess Parvathy has a separate shrine on the third 'praharam'. She is worshipped as 'Unnamulai Ambal'.
Annamalai achieves its importance as a venerated and holy place as it is mentioned in Hindu mythology and legends and also by its association with saints, sages and religious men and women who have sung the praises of the deity in their devotional outpourings. The temple also has an important place as a repository of historical chronicles with its large amount of inscriptions on its walls and pillars. These are studied and researched by historians in an attempt to understand the life in the country centuries ago.
Once there was a dispute between Lord Brahma and Lord Vishnu as to who was superior. This created untold suffering among all living things as their respective duties of creation and protection were being left unattended. Lord Shiva in order to put an end to this dispute appeared before them as fire in the shape of a glowing mountain.. The two who were quarrelling did not realise who or what this 'mountain of fire' was. So they decided to search for the 'Aathi' (beginning) and the 'Antham' (end) of this 'Jothi' and whoever succeeded first would be declared the superior god. Lord Brahma took the form of a swan and flew upwards in search of the beginning and Lord Vishnu took the form of a 'Varaha' (wild boar) and went burrowing in the earth in order to find the end. Each after flying high and borrowing low failed in his attempt to find the beginning or the end. Brahma did not want to concede defeat. While coming down he saw a petal of 'Thalampoo' floating in the air. He asked the flower to be his witness that he had seen the beginning. The flower agreed to his request. They arrived together and found Lord Vishnu and told Him that Brahma had seen the top and this flower 'Thalampoo' was the witness. At this juncture the 'Jothi' transformed itself as Lord Shiva and admonished Brahma for telling lies and the 'Thalampoo' for bearing false witness. He also decreed that no temples would be dedicated for Lord Brahma and that 'Thalampoo' should never be offered in worship.
Brahma and Vishnu realising their mistake prayed to Lord Shiva to remain there as a 'Jothi lingam'. Thus every year during the Tamil month of 'Karthigai' (November/December) on the 'Karthigai' day a blazing fire is lighted on the top of the hill to celebrate the appearance of Lord Shiva as 'Jothi'. This occasion is an important day in the calendar of Thiruvannamalai.
There is also another legend that says that Goddess Parvathy once playfully closed the eyes of Lord Paramasivan. This caused the entire universe to become dark and all activities to cease. This made Lord Shiva angry and in order to chastise Parvathy, she was banished to the earth. She came upon this earth and arrived at Kancheepuram. Here she fashioned a Sivalingam in sand and prayed to Lord Shiva to forgive her and take her back. Lord Shiva was pleased with her devotion and prayer and asked her to go to Thiruvannamalai and pray to Arunachaleswarar. Goddess Parvathy arrived at Thiruvannamalai and was finally united with the Lord by taking half his body on the left. This transformation of half Parvathy and half Shiva is called 'Arthanareeswarar'.
Though this temple is famous as a Shiva temple, there is a shrine dedicated to Lord Subramanya in the outer 'veethy' The deity is called 'Kambaththu Ilayanar'. This is where Lord Subramanya appeared on a pillar. The legend is as follows. Arunagirinathar, the saint poet and an ardent devotee of Lord Subramanya, lived in Thiruvannamalai. He had squandered his wealth by his youthful waywardness and had contracted an incurable disease as a result. Finally he got fed up with his lot and climbed a temple tower and jumped from there in an attempt to kill himself. Lord Subramanya stopped him falling in mid-air and blessed him with wisdom and set him in a path of piety and devotion. From that day he brought forth his devotion and piety in the form of devotional verses called 'Thiruppugal'. This brought fame and respect to Arunagirinathar. A court member of the king of Thiruvannamalai named Sambathanthan got jealous of Arunagirinathar. He was a devotee of Goddess Sakthi. He challenged Arunagirinathar for a contest. He said that he would make Goddess Sakthi appear before him and challenged Arunagirinathar to do the same with his Lord. Arunagirinathar accepted the challenge. When Sambathandan prayed to Goddess, She appeared in front of him but only he could see her. When Arunagirinathar prayed to Lord Subramanya His figure appeared on a stone pillar for everybody to see. It is this pillar with the image of Lord Subramanya which is installed in the sanctum of Kambathu Ilayanar temple.