In this study, a tracking and pointing control system with a dual-FSM (fast steering mirror) two-dimensional flexible turntable composite axis is proposed. It is applied to the target-tracking accuracy control in a GI LiDAR (ghost imaging LiDAR) system. Ghost imaging is a multi-measurement imaging method; the dual-FSM GI LiDAR tracking and pointing imaging control system proposed in this study mainly solves the problems of the high-resolution remote sensing imaging of high-speed moving targets and various nonlinear disturbances when this technology is transformed into practical applications. Addressing the detrimental effects of nonlinear disturbances originating from internal flexible mechanisms and assorted external environmental factors on motion control’s velocity, stability, and tracking accuracy, a nonlinear active disturbance rejection control (NLADRC) method based on artificial neural networks is advanced. Additionally, to overcome the limitations imposed by receiving aperture constraints in GI LiDAR systems, a novel optical path design for the dual-FSM GI LiDAR tracking and imaging system is put forth. The implementation of the described methodologies culminated in the development of a dual-FSM GI LiDAR tracking and imaging system, which, upon thorough experimental validation, demonstrated significant improvements. Notably, it achieved an improvement in the coarse tracking accuracy from 193.29 μrad (3σ) to 87.21 μrad (3σ) and enhanced the tracking accuracy from 10.1 μrad (σ) to 1.5 μrad (σ) under specified operational parameters. Furthermore, the method notably diminished the overshoot during the target capture process from 28.85% to 12.8%, concurrently facilitating clear recognition of the target contour. This research contributes significantly to the advancement of GI LiDAR technology for practical application, showcasing the potential of the proposed control and design strategies in enhancing system performance in the face of complex disturbances. © 2024 by the authors.