In response to the growing requirements for micro-positioning stages in micro-nano manufacturing and precision metrology, a high-precision motion control system is specially designed based on the structural characteristics, driving mode, and performance requirements of a 6-DOF micro-motion stage with nanometric resolution. Circuit output performance tests and overall drive control effect tests were subsequently conducted. The micro-motion stage features a three-layer structure with hollow interior to facilitate optical paths of 3D laser interferometry. It utilizes flexure hinges in combination with piezoelectric actuators, adopting hybrid serial-parallel driving mode. Its motion control system based on an ARM processor includes main control, signal processing, linear amplification, power supply and protection modules, providing multi-channel output, high voltage stability, low noise, and superior resolution. Experimental characterization demonstrates that the system delivers an output range of 0~170 V, noise of 0.2 mV, linearity error of 0.12%, and an operational bandwidth of 0~100 Hz (with 16 μF load). The stage achieves a displacement stroke exceeding 20 μm, a displacement resolution of 0.5 nm, and a rotational resolution of 0.1″. The micro-motion stage and its motion control system demonstrate strong applicability for nanometer and sub-nanometer level positioning and orientation control in the areas of ultra-precision machining and high precision measurement, such as the measurement triggering and attitude compensation of a cross-scale micro-nano coordinate measuring machine (CMCMM) system.