In the design process of lightweight harmonic drive system, low-frequency resonance generally affects controller design, and restricts system servo performance. In the design stage of system, it has great significance that the resonant frequencies and dynamic performances could be predicted. This paper presents a modeling method of harmonic drive system which has low-frequency resonance. Takes an uniaxial harmonic drive system as example to describe the implementation process of the modeling method. The dynamics model of harmonic drive system has been built. Using Ansys, Recurdyn and Matlab, the rigid-flexible coupling dynamics simulation model of system has been established. The simulation model analysis and the actual system experiment have been done respectively. Comparing the simulation and experiment results, it shows that: the open-loop time-frequency domain characteristics and the structural modals of simulation and experiment results are basically consistent. Using this method, the resonant frequency and dynamic performance of harmonic drive system can be predicted in the system design stage, and improve design efficiency.