The structural flexibility, nonlinear friction, and backlash are the major factors limiting the control performance of precision transmission systems. If uncompensated, these factors compromise the positioning and tracking accuracy of precision transmission systems and even cause limit cycles and oscillation. In this article, a framework for integrated design from dynamic modeling to controller design is proposed. A multi-state dynamic model is presented, which can unify the modeling for a multi-state, discontinuous system including the motor state, the motion state, the mechanical contact state, and the friction state. Then, a control design method related to the dynamic modeling using perturbation separation of the model parameters is presented. Using the proposed modeling method, a continuous dynamic model is established to include all different partition models. The model comprehensively describes the mechanical and electrical characteristics of the precision transmission system. A robust controller is designed using the proposed control method. Experimental results demonstrate that the proposed modeling method is accurate and the proposed control method significantly improves accuracy and robustness of the controller compared to traditional control methods.