The invention discloses a surgical instrument calibration system and method for navigating surgery. The calibration system includes a navigator, a calibration table, a calibration table reference mark, a surgical instrument reference mark, a computer and a display. When calibrating, only the surgical instrument is held and fixed on the standard position on the calibration table, the structural parameters of the calibration table are used, all the reference mark images of the surgical instrument and the calibration table are collected simultaneously by the navigation instrument at one time, andthe axial vector and the tip position of the surgical instrument are directly calculated by the geometric analysis algorithm software, the template position of the surgical instrument is recorded, and the calibration of the surgical instrument is completed. All parameters can be calibrated by this system in one time, which can greatly reduce the number of times of image acquisition, simplify thecalibration process, improve the accuracy and reliability of calibration, save time and labor, and make the whole calibration process with high efficiency and small error. The calibration process is simple and easy to operate, which can obviously reduce the risk of calibration failure and improve the success rate of calibration. The calibration table is simple in structure, accurate and reliable,and easy to manufacture and use.