To solve the problem of precise positioning of carp brain tissue coordinates, it is proposed in this paper for a method for transforming the coordinates of magnetic resonance imaging of carp brain tissue into the coordinates of electrode implantation using a brain stereotaxic apparatus. In this study, the 3.0T magnetic resonance imaging instrument was used to scan the carp brain. We independently established the three-dimensional positioning coordinate system of the brain, the three-dimensional coordinate assistance system of skull surface and the three-dimensional coordinate assistance system in brain tissue. After two coordinate transformations, the magnetic resonance image coordinates of the brain electrodes implantation sites were converted into the three-dimensional stereotactic coordinate system to guide the electrodes implantation. The experimental groups were divided into two groups, A and B. Group A was the group of magnetic resonance imaging apparatus combining with the brain stereotaxic apparatus, and group B was the group of brain atlas combining with the brain stereotaxic apparatus. Each group had 20 tails of carps (n = 20). This two methods were used to implant the electrodes into the cerebellar motor area. The underwater experiments of the carp robots were carried out to test the two methods. The results showed that the accuracy of the implanted electrodes were 90% in group A and 60% in group B. The success rate of group A was significantly higher than that of group B (P < 0.05). Therefore, the new method in this paper can accurately determine the coordinates of carp brain tissue.