The effect of deep brain stimulation (DBS) surgery treatment for Parkinson's disease is determined by the accuracy of the electrodes placement and localization. The subthalamic nuclei (STN) as the implant target is small and has no clear boundary on the images. In addition, the intra-operative magnetic resonance images (MRI) have such a low resolution that the artifacts of the electrodes impact the observation. The three-dimensional (3D) visualization of STN and other nuclei nearby is able to provide the surgeons with direct and accurate localizing information. In this study, pre- and intra-operative MRIs of the Parkinson's disease patients were used to realize the 3D visualization. After making a co-registration between the high-resolution pre-operative MRIs and the low-resolution intra-operative MRIs, we normalized the MRIs into a standard atlas space. We used a special threshold mask to search the lead trajectories in each axial slice. After checking the location of the electrode contacts with the coronal MRIs of the patients, we reconstructed the whole lead trajectories. Then the STN and other nuclei nearby in the standard atlas space were visualized with the grey images of the standard atlas, accomplishing the lead reconstruction and nerve nuclei visualization near STN of all patients. This study provides intuitive and quantitative information to identify the accuracy of the DBS electrode implantation, which could help decide the post-operative programming setting.