This paper presents a method of motion tracking of highly dynamic multi-link systems with Inertial Measurement Units (IMU) embedded with magnetometers in spaces with nonuniform magnetic fields. As IMUs may accumulate error due to drift, magnetometers are used to correct orientation estimation. With usual magnetic distortion compensated for assuming magnetic field uniformity of the space prior to motion measurement, this method introduces real-time calibration using two oppositely facing triaxial magnetometers, along with triaxial accelerometer and gyroscope. Using the described array of magnetometers, local hard iron distortion can be measured at any position. Along with inconsistency of distortion throughout a nonuniform space, the measured direction of magnetic north may also change. Rather than assuming a constant magnetic north direction like conventional methods, a sensor model for the magnetometer using the last measured magnetic north direction as the reference heading is used to compensate for the inconsistency. The proposed sensor suite and model reduces the error by half an order of magnitude less than conventional magnetometer usage. With the proposed method, drift is corrected for, even in nonuniform magnetic fields.