A motion estimation method and system for a mobile body are provided. The method includes: obtaining magnetic field information from compass information of the mobile body; comparing the magnetic field of the mobile body with a predetermined value and determining whether a position of the mobile body belongs to a specific region according to the comparison result; and estimating a direction of the mobile body by determining whether a compass azimuth angle is used for direction estimation of the mobile body according to the determination result. The system, in which a gyro, odometers, and compasses are installed, comprises: a magnetic field calculator calculating the magnitudes of magnetic fields of the mobile body; a magnetic field comparator obtaining differences between the magnitudes of the magnetic fields and the magnitude of the geomagnetic field and comparing the differences with the first threshold value; a geomagnetic region determiner determining whether a position where the mobile body exists belongs to a region where the geomagnetism works according to the comparison result; and a moving direction estimator estimating a moving direction of the mobile body by determining whether or not to use azimuth angles of the compasses for direction estimation of the mobile body according to the determination result.