A surgical navigation system based on IGSTK (Image-Guided Surgical Toolkit) that guide medical robot to drill pedicle screw into vertebra precisely is presented. The surgical location device used is NDI Polaris Vicra® optical tracking system and the assistance robot is KUKA® Robot KR 5 sixx R650. Message communication between the navigation system and KUKA robot is implemented based on OpenIGTLink protocol client-server model. Multiple tracked tools can be tracked automatically by state-machine mechanism in a safe manner. To overcome the line of sight limitation of optical tracking system, a new instrument that we called it two-face instrument model has developed to enlarge the rotation angle of the tracked tool. The experiment showed that the navigation could guide robot to execute precise surgical operation in a simple and safe mode.