There are four main differences between Avatar anatomy and the anatomy of the Na'vi. First and most importantly, Avatars possess neurocircuitry similar to the human brain. This allows the controllers to control their Avatars through telink. The second difference is that Avatars have five digits on their hands and feet, like humans, where Na'vi only have four. Both of these differences are the result, intentional or otherwise, of the genetic modification of the Avatar bodies.
Thirdly, the shape of the skull is different, Avatars have a humanized skull meanwhile Navis do not.
The fourth most noticible difference is that Na vis' queues originate at the top of the skull while Avatar's queus start much lower, near the base of the brain. This is apparent by analysing where the plait on different individuals terminate; Jakes plait starts where humans normally wear a pony tail where as the plait on all Na vi originate much higher. Further evidence is shown when Jake pilots the Avatar for the first time and a scan of both his Human and avatar brains are shown on a datapad. There is a cluster of nerves extending from the base of the avatar's brain.
The Na vi refer to Avatars as dreamwalkers.