The effects of ionizing radiation and celestial perturbation force can cause current and position disturbances in the voice coil motor (VCM) and motion loader of the fast steering mirror (FSM) system on a space-based platform, which can affect the steady-state accuracy and tracking accuracy. To reduce the influence of disturbance, disturbance observations (DOBs) are introduced into the current and position paths to realize the suppression of specific disturbances. First, the influence of output accuracy caused by disturbances in a space-based environment are analyzed. Then, DOBs are introduced into the current and position output paths. The new systems are analyzed, and the disturbance controllers are designed. Finally, the theoretical data are simulated and compared with the test results of the rigid–flexible coupling virtual prototype control system. The results show that under the effect of dual DOB control, the disturbance suppression ability is 92.59% at 200Hz current and 40Hz position disturbance frequency. The error between the virtual prototype test results and the theoretical calculation result is within 10%.