Brain computer interface (BCI) is one of the important research methods in the fields of brain cognition, brain medicine and brain-like research,where the precise implantation of microelectrodes is a necessary prerequisite and important guarantee. To meet the demand for precise implantation of microelectrodes in the somatosensory and cerebral motor cortex of SD rats, this paper designs a high-precision and high-flexibility precise implantation system which integrates target recognition, cranial drilling, and precise implantation. Firstly, the machine vision method is used to realize high-precision target recognition by identifying the key points of rat cranial bone, and establishing the coordinate system for obtaining the point cloud information of rat cranial bone. Then, based on the hand-eye system, a robot kinematics solution model is established to achieve high-precision positioning of the motion base. Finally, the precise implantation of microelectrodes is achieved through the drilling micro-movement of penetrating the cranial bone or making a window, and the clamp high-precision micro-movement of implanting the electrode. The experimental results show that the drilling and planting module can drill through the skull quickly and implant the electrode to the target area accurately and stably.