Concerning the problem that too many transitional links and complex parameter solving process existed in camera calibration of the surgical navigation based on C-arm, a new method that completely ignored the camera model was proposed. In this method, the camera model was completely ignored, and the transition link in the process of solving mapping parameters was simplified, which increased the efficiency. In addition, the camera calibration was achieved by distinguishing the projection data from the calibration target which has double-layer metal ball. In the calibration point verification experiment, it can be proved that the residual error of each test point was no more than 0.002 pixels; in the navigation validation experiment, probe point and perforation test were successfully implemented with the established preliminary experiment platform. The experimental results verify that the proposed camera calibration method can meet the accuracy requirements of surgical navigation system.