This article presents the design of a motion control system for seated lower-limb rehabilitation training. The system is composed of lower limb exoskeleton, motor drive circuit, program of motion control, and so forth. The power of lower limbs joints is provided by six motors. The PCI-1240 motion control card is used as the core. This study achieved repetitive rotation training and gait trajectory training of lower limbs joints, of which the velocity, angle and time can be accurately controlled and adjusted. The experimental results showed that the motion control system can meet the requirement of repetitive rehabilitation training for patients with lower limb dysfunction. This article provides a new method to the research of motion control system in rehabilitation training, which can promote industrial automation technique to be used for health care, and conducive to the further study of the rehabilitation robot.