The hill on which the Kamakhya temple exists is known as Nilachal or Blue Hill. The overall architectural shape of the present Kamakhya temple, which was rebuilt in 1565 AD using the ruins of the 11th-12th century stone temple, was modelled by a combination of two different styles, namely the traditional Nagara or North Indian and the Saracenic or Mughal. Thus, being an unusual combination, which came into existence on this famous Shakti temple of India, it is named as Nilachal style of architecture. Incidentally, this temple-type became a dominant pattern in the construction of temples through royal patronage in later times in Assam. The reason behind the development of this new type by violating the orthodox Nagara tradition is explained in the 17th century AD compilation Darang-Rajvanshavali. It states that when the masons sent by Koch king Narayana (AD 1540-1585) from Kochbehar failed in their several attempts to recreate the shikhara or domed portion using the original stone blocks, they finally opted to use bricks following the Saracenic technique of the round dome. But to give a new look, they changed the global shape to a sixteen-sided polygon decorated with horizontal stripes. Apparently, this gave rise to a new architectural style with popularity in Assam.

The Kamakhya temple has some important peculiarities. It is the only temple in Assam with a fully developed ground-plan. It has five chambers, viz., Garbhagriha or sanctuary, Antaral or vestibule, Jagamohana or main chamber, Bhogamandir or ritual hall and Natamandir or opera hall for performance of traditional dance and music associated with Shakti shrines. This last chamber was added to the temple complex by the Ahom king Rajeshwari Singha (1751-69 A.D.) in 1759 A.D. It is interesting to note that the superstructure of each of the above chambers exhibits different architectural features. While the main temple has a modified Saracenic dome, the Antaral has a two-roofed design similar to traditional thatched huts; the Bhogamandir (also called Pancharatna) has five domes similar in appearance to the main temple and the Natamandir has a shell-roof with a finial similar to some temporary Namghars or prayer halls found in Assam.

It is noteworthy that these five types of superstructures individually served as models for designing the shikharas of many temples throughout Assam. Thus, the renovation of the Kamakhya temple of 1565 AD ushered in a new phase of architecture that filled late-medieval Assam with a variety of temple forms.

The holy town of Kamakhya has many temples of the historic period, which house the Peethas or shrines of the ten Mahavidyas or the ten aspects of Goddess Kamakhya. Besides, here we find five Shiva temples, one Vishnu temple and a few temples and shrines of other deities, but their shikharas are either in the traditional Naraga or Rekhadeul form or in the Nilachal style, imitating the main Kamakhya temple.