In this paper, a cascade double-loop control (DLC) combined with modeling compensation methods is proposed to improve the tracking precision of the multiaperture imaging system (MAIS). The application of the flexible thin-wall ring mechanism in the coupling rotating prism (CRP) system causes a series of tracking and pointing challenges. Disturbances such as friction, shaft deformation, and model perturbation significantly deteriorate the tracking and pointing accuracy of the CRP. Two different modeling compensation methods that are interfaced with classical DLC are proposed to guarantee the tracking precision of the MAIS. Moreover, the disturbance observation and compensation performance of two different modeling compensation methods are analyzed and compared. Finally, simulation and experiment results indicate that the proposed control methods, especially model compensation based on speed close-loop control, obtain the best performance for disturbance rejection in the MAIS.