To improve the general performance of knee-joint rehabilitation trainer (KRT), an embedded control system for the KRT based on embedded linux OS was designed, taking 32bits processor S3C2440 as core control unit. The overall scheme, hardware and software architectures of the system were designed. The key technologies dealing with the embedded linux drivers and the applications based on QT were studied. Experimental results proved that the designed embedded control system is reliable, easy to handle, and can control the KRT to realize isokinetic continuous passive motion and isokinetic active resistance motion. This can provide the guidance for the design of embedded control system in similar medical devices.