In this paper, a design of modularized flexible joint servo controller on-chip for a space manipulator system is presented. First of all, the structure and sensor system of dual-joint is introduced. The structural optimization design of the joint torque sensor is carried out with the help of the ANSYS program for weight minimization. Next, the features of the hardware system for the dual-joint controller are described. All sensor information collection within the joints are obtained with FPGA hardware logic elements using System-on-a-Programmable-Chip technology, and the joint space trajectory planning and position control are realized by Nios II soft-core processor, which is embedded in FPGA. Finally, experimental results demonstrate the effectiveness of the compact joint servo controller for the space manipulator system.