In order to improve the trajectory tracking precision and the vibration suppression capability of flexible joint robots, a passivity theory based flexible joint controller is proposed. The controller is verified and simplified in Simulink environment in order to make it more suitable for the robot with multiple degrees of freedom (DoF). Experiments are conducted on a 7-DoF robot with DSP+FPGAs structure, and the nonlinear and linear parts are calculatd in digital signal processor (DSP) and field programmable gate array (FPGA) separately, which avoids the performance change of the joint controller due to the increasing DoF. The experiment results show that comparing with the PD (proportional-derivative) controller, the proposed controller has the advantages of lower torque fluctuation, faster vibration suppression and higher static accuracy.