Neurosurgery navigation system consists of an image workstation, infrared optical positioning device and surgical instrument components. The system can use the patient CT/MRI images to develop preoperative surgical plan, choose the best surgical approach, in surgery it can rely on the three-dimensional patient images and optical locator, avoiding critical organizations and major functional areas, to make surgery smaller incisions, more thorough, more secure. The development consists of the following steps: image group management, displaying three orthogonal plane (transverse, sagittal, coronal), 3D reconstruction, image segmentation, three-dimensional drawing, 3D image space and operative space registration structure and function like image fusion. The main work and contribution of this paper is: 1. three dimensional reconstruction using linear interpolation instead of the bilinear interpolation, improve image clarity; 2. 3D rendering, pixel reconstruction filter using windowing, then directly draw pixels to improve rendering speed; 3. human-computer interaction by reducing the resolution to accelerate and achieve real-time three-dimensional rotation; 4. 3D image space and space operation registration method using landmarks, enhanced registration reliability; 5. with fusion of the function and structure image surgery can be used to avoid important functional areas, reduce the risk of disability.