In this paper, a tracking and pointing control system with dual-FSM (fast steering mirror) composite axis is proposed. It is applied to the target-tracking accuracy control in a 3D GISC LiDAR (three-dimensional ghost imaging LiDAR via sparsity constraint) system. The tracking and pointing imaging control system of the dual-FSM 3D GISC LiDAR proposed in this paper is a staring imaging method with multiple measurements, which mainly solves the problem of high-resolution remote-sensing imaging of high-speed moving targets when the technology is transformed into practical applications. In the research of this control system, firstly, we propose a method that combines motion decoupling and sensor decoupling to solve the mechanical coupling problem caused by the noncoaxial sensor installation of the FSM. Secondly, we suppress the inherent mechanical resonance of the FSM in the control system. Thirdly, we propose the optical path design of a dual-FSM 3D GISC LiDAR tracking imaging system to solve the problem of receiving aperture constraint. Finally, after sufficient experimental verification, our method is shown to successfully reduce the coupling from 7% to 0.6%, and the precision tracking bandwidth reaches 300 Hz. Moreover, when the dis-tance between the GISC system and the target is 2.74 km and the target flight speed is 7 m/s, the tracking accuracy of the system is improved from 15.7 μrad (σ) to 2.2 μrad (σ), and at the same time, the system recognizes the target contour clearly. Our research is valuable to put the GISC technology into practical applications. © 2022 by the authors. Licensee MDPI, Basel, Switzerland.