The temple consists of four chambers: garbhagriha and three mandapas locally called calanta, pancaratna and natamandira. The garbhagriha has a pancharathaplan and rests on plinth moldings that are similar to the Surya Temple at Tezpur, above which are dados from a later period of the Khajuraho or the Central Indian type, consisting of sunken panels alternating with pilasters.  The sikhara in the shape of a bee-hive, which is characteristic of temples in Lower Assam. The inner sanctum, the garbhagriha, is a cave below ground level and consists of no image but a rock fissure:

The garbhagriha is small, dark and reached by narrow steep stone steps. Inside the cave there is a sheet of stone that slopes downwards from both sides meeting in a yoni-like depression some 10 inches deep. This hallow is constantly filled with water from an underground perennial spring. It is the vulva-shaped depression that is worshiped as the goddess Kamakhya herself and considered as most important pitha (abode) of the Devi.

The garbhaghrihas of the other temples in the Kamakhya complex follow the same structure—a yoni-shaped stone, filled with water and below ground level.

The current structure has been built during the Ahom times,with remnants of the earlier Koch temple carefully preserved. Temple was destroyed during the middle of second millennium and revised temple structure was constructed in 1565 by Chilarai of the Koch dynasty in the style of medieval temples. The current structure has a beehive-like shikhara characteristic of lower Assam with delightful sculptured panels and images of Ganesha and other Hindu gods and goddesses on the outside. The temple consists of three major chambers. The western chamber is large and rectangular and is not used by the general pilgrims for worship. The middle chamber is a square, with a small idol of the Goddess, a later addition. The walls of this chamber contain sculpted images of Naranarayana, related inscriptions and other gods. The middle chamber leads to the sanctum sanctorum of the temple in the form of a cave, which consists of no image but a natural underground spring that flows through a yoni-shaped cleft in the bedrock.