The jutsu which Orochimaru used is called Juinjutsu. Orochimaru was unable to use Sage Mode and thus had to create an alternative way to make use of Senjutsu.
In addition to his various test subjects, Orochimaru gave cursed seals to some of his most powerful and unique followers, either to enhance their abilities or to prepare them for becoming potential host bodies. To apply a cursed seal, Orochimaru bites the recipient, doing so with the aid of his sharp fangs and extendible neck. The seal then appears on the body of the victim near the puncture wound before causing them to lose consciousness.
Now try recalling the concept of Bunshin no Jutsu. When clones are created, it has mind of their own. As a result, when it is released, the original would get the details of clone's experience. Clearly Orochimaru's technique is not Bunshin. It's much more evolved than that. He shares a portion of his power in the host's body and tries to reside in the body. So naturally, it has a different mind.
Try recalling the incident during Kabuto and Sasuke fight. After Orochimaru was revived from Anko Mitarashi's body by Uchiha Sasuke, he said that he had been seeing the entire war from Anko's body, which clearly showed that he was mentally active inside the host's body.