To effectively guide the design of fast steering mirror (FSM), the research of theoretical modeling and simulation analysis for FSM was carried out. Compared with the single degree of freedom motion model, the multiple degrees of freedom motion differential equation of a two-axis FSM was built based on the dynamics analysis, and the transfer function of the controlled object as well as isolation transfer function to the base disturbance were derived. The influence of structure resonance frequency on the characteristics of the controlled object was simulated. When the rotation natural frequency was high, the controlled object was an under-damped system which had resonance peaks. The simulation model was built for the FSM control system with the structural characteristics. The influences of the load centroid deviation from the flexible hinge support center and the structural resonance frequency on the disturbance rejection performance were researched. The disturbance rejection performance would be better when the natural frequency of non-working shaft was higher. Generally, the frequency at the gain junction of the servo system is more than 2 times, and the natural frequency of the working shaft should be selected by weighing the disturbance rejection performance and motor torque constraints. Finally, the correctness of the simulation model was verified via the physical vibration experiments.