In engineering application, the control strategy based on the controlled object mathematical model is adopted to design the controller of electro-optical tracking systems. If the model identification is accurate and how to develop controller design are become system difficulty. A data signal processor (DSP) controller is used to perform full digital transfer function test to the electro-optical tacking system, process test data on-line to get the strategy mathematical model. The desired system parameters are received by DSP controller to calculate the corrected parameters automatically and finish the design of the controller framework. According to features of the tracking target, combined with the characteristics of tracking errors and engineering experiences, the quasi-speed and accelerated speed compensation algorithms are proposed to optimize the controller, which is has already been used in a certain electro-optical tracking system successfully. The design method of high accuracy controller based on model identification design has the characteristics of simple, practical and without additional cost, which improves system tracking accuracy and has better operation effect.