In order to accurately implant the brain electrodes of carp robot for positioning and navigation, the three-dimensional model of brain structure and brain electrodes is to be proposed in the study. In this study, the tungsten electrodes were implanted into the cerebellum of a carp with the aid of brain stereotaxic instrument. The brain motor areas were found and their three-dimensional coordinate values were obtained by the aquatic electricity stimulation experiments and the underwater control experiments. The carp brain and the brain electrodes were imaged by 3.0 T magnetic resonance imaging instrument, and the three-dimensional reconstruction of carp brain and brain electrodes was carried out by the 3D-DOCTOR software and the Mimics software. The results showed that the brain motor areas and their coordinate values were accurate. The relative spatial position relationships between brain electrodes and brain tissue, brain tissue and skull surface could be observed by the three-dimensional reconstruction map of brain tissue and brain electrodes which reconstructed the three-dimensional structure of brain. The anatomical position of the three-dimensional reconstructed brain tissue in magnetic resonance image and the relationship between brain tissue and skull surface could be observed through the three-dimensional reconstruction comprehensive display map of brain tissue. The three-dimensional reconstruction model in this study can provide a navigation tool for brain electrodes implantation.