Objective Precision of the surgery navigation system is influenced by multiple factors. This paper focuses on the precision of electromagnetic surgery navigation system. Methods By studying the basic composition of surgery navigation system and the coordinate transformation method in the system,we propose that the error of positioning system and the error of surgery registration are two main error sources in the navigation system. We design a series of precision experiments to test the system precision including positioning system,surgery registration and the whole system. Results The precision of the electromagnetic positioning system is (0.19±0.15) mm and that of the whole system is (1.44±0.39) mm. The results show that we can get a desired registration effect if we use 7 to 10 markers to cover the focus of the patient’s skull. Finally,four feasible methods are proposed to improve the system precision,including optimizing image processing,surgery registration,brain tissue correction algorithms and reducing interference sources. Conclusions The precision of electromagnetic surgery navigation system is influenced by many factors,such as positioning system,three-dimensional reconstruction and surgery registration. The precision of the surgery navigation system described in this paper reaches the demand of general surgical navigation systems.