Focusing on the limitations of the low-cost strapdown inertial navigation system (SINS) which just can provide accurate navigation information during a short time, and considering the passive navigation demand in war, a low-cost SINS/Magnetometer (MR) tightly-coupled navigation system based on the Kalman filter is proposed. Because MR is easily affected by the magnetic field around to generate the magnetic deviation, the tightly-coupled Kalman filter is used to evaluate and compensate the magnetic deviation parameters through the WMM2010 magnetic model and the horizontal attitude provided by the SINS. As a result, the accuracy of heading attitude output by the MR has increased. Furthermore, the precision of the low-cost SINS/MR tightly-coupled navigation system is improved. Finally, the field-test over 25 minutes verifies the algorithm: the position, velocity and heading errors provided by the tightly-coupled navigation system are less than 10 m, 0.2 m/s and 0.3 deg. So the system offers significant contribution to the practical engineering application.