Based on the developed rehabilitation manipulator, study on the control system is carried out, such as embedded system platform with the ARM microprocessor S3C2410as its core, motor control module and data acquisition module based on serial peripheral interface (SPI) bus, control software and graphical user interfaces (GUI) etc. According to the mechanical system, a sensor system is also designed to realize the function of acquisition of rehabilitation dada during rehabilitation motion. The test proves the feasibility of the system which can be used in clinic in future.