GNSS and ARS are the most common sensors in low-end UAVs. However, these sensors are vulnerable to built-in errors and cannot measure the body heading independently. The GNSS/INS cannot fully compensate the IMU errors in initial alignment process and rectilinear flights. For an unmanned helicopter, a magnetometer can be more useful than any other sensors to obtain heading information. However, the electric motor which drives small helicopter UAV keeps the magnetometer from reading the pure magnetotelluric vector. This paper shows the effects of electric motor on the magnetometer readings, and presents a method to compensate the effects. The results are verified with flight test data. The simulation and experimental results in this paper proves that aiding GNSS/INS with magnetometer increases observability and improves accuracy.