Optimized control of remanufacturing assembly process in a dynamic and uncertain environment has been recognised as a big challenge for remanufacturer. Therefore, an integrated optimization control method for reassembly system is proposed. The state space model of the remanufacturing assembly process and the transfer matrix of reassembly are constructed to characterize the transfer mechanism of reassembly process. Then, an optimization control model based on dynamic programming is established to realize online guidance of reassembly station. Finally, the method is applied in reassembly line of crankshaft remanufacturing, and the feasibility and effectiveness are verified. The results show that this method can effectively improve the quality of remanufactured products by 5.27%, and reduce the cost of reassembly system by 2.76%. Moreover, the method provides theoretical and methodological support for the core competitiveness of remanufacturing enterprises.