The structure of seeker servo system and the function of its servo loop including locking, stabilization, searching and tracking were analyzed. Based on the structure of dual DSP, a controller for seeker control system was designed in order to realize the function of communication, disturbance isolation and target tracking. And the hardware configuration and software structure were introduced. The theory of disturbance isolation and target tracking of seeker servo system was analyzed. A method for designing a digital controller based on dSPACE hardware-in-the-loop simulation system was proposed by designing a controller for yawing stabilization loop. Experimental results of disturbance isolation and target tracking show that the digital control system for seeker designed in this paper has good performance, and can satisfy the requirements of disturbance isolation and target tracking function of seeker.