This paper proposes the calibration method of magnetic field sensor using inertial sensor. The calibration of magnetic field sensor is effectiveness as the compensation method of static magnetic disturbance. In the prevous studies, the calibration methods using the special devices have been proposed. On the other hand, the magnetic field sensor is attached to the body segment in body motion measurement. It is necessary to develop the calibration method for body motion measurement. In this study, we developed the calibration method of magnetic field sensor for body motion measurement. This method can estimate the calibaration parameter of magnetic field sensor by applying the inertial sensor output to Extended Kalman filter. Futhermore, This method was extended to the method considering the alignment error between the inertial and magnetic field sensors.