Abstract: The present invention relates to a method for three-dimensional image reconstruction of basal ganglion. A novel geometrical algorithm has been developed to calculate the correction coordinates of the target based on the reference axial shift in the CT scan coordinate system. Furthermore, wavelet transform along with interpolation techniques are used to obtain continuous sectional images and three-dimensional image reconstruction is then performed to form the stereotactic atlas of basal ganglion. Therefore, the stereotactic atlas of basal ganglion established in this invention can be used as references for assisting operation and training for neurosurgeons.