In missiles design process, in order to obtain the dynamic parameters of the missile in flight. We usually use the geomagnetic sensor to measure the attitude information of the projectile. However, there are some errors of three-axis magnetometers which we commonly used. Therefore, the calibration of magnetometers measuring error is seems very important. This article put forward a new method which to calibration the time-varying error of three-axis magnetometers. This method is an expansion for the existing method which is constant error. So that the magnetometer can be used for calibration with time-varying bias. This method is particularly suitable for complex electromagnetic environment onboard measurement system that can effectively calibration the measure error of three axis magnetometer. Finally, the results were verified by simulation data.