Magnetic navigation system needs magnetic resistance sensor to measure the earth's magnetic field strength as the navigation information, accurate measurement of the geomagnetic field information is one of key technologies of geomagnetic navigation. As the characteristics of magnetic resistance sensor and the production installation, they must be calibrated to get accurate and effective measurement of magnetic field. In this paper, the magnetic sensor calibration error source was analyzed, and the 12-position combined with accelerometer information calibration method was used for magnetic sensor calibration. The field experiment shows that the use of this method can make the max error less than 20 nT, and this method is easy and effective.