To counteract the hysteresis introduced by a harmonic drive and to improve the precision of a Double Gimbal Magnetically Suspended Control Moment Gyroscope (DGMSCMG) gimbal system, a modeling method of hysteresis characteristics of the harmonic drive was proposed. Firtly, the first-order reversal curve method was used to capture the outputting torque of the flexible gear and the torsion angle of the harmonic drive and to obtain the data to establish the hysteresis model of the harmonic drive, in which the outputting torque of the flexible gear was estimated by a system dynamic model instead of a direct measurement from the torque sensor. Then, the Preisach model was used to establish the hysteresis relationship between the outputting torque of the flexible gear and the torsion angle of the harmonic drive. Finally, the modeling was discretized and its weighting function was then well mapped by applying mathematical implementation.Furthermore, a discrete recursive algorithm of the model was also provided for simply programming and further on-line controlling. Results of the carefully designed experiments conducted on the DGMSCMG show that the deviation between calculated and measured torsion angles is limited within a 0.005° range, and the MSE value is under (0.000 83%)°. These results show that the model well predicts the hysteresis of the system.