Automobile and logistics are the two critical restructuring and invigorating industries in China． In the context of assembly plant capacity expansion，with the purpose of improving the system performance，this paper elaborates on the optimal design of key operations in the logistics mode of auto parts milk run and cross dock dealt with by a 3PL company． We build a simulation model which integrated the operations of milk run and cross-docking based on practical research data． Further，we propose an optimization algorithm that uses sequential bifurcation and Response surface methodology (SB-RSM) of the design and analysis of simulation experiments theory． The results of specified simulation design and runs indicate that the logistics performances are greatly improved if the 3PL simply optimizes the key operations，which helps to reduce the workload of the 3PL． The proposed SB-RSM shows higher efficiency and efficacy than classical RSM． This study contributes to decision making concerning supporting automobile parts 3PL Company when the automobile assembly plant capacity expands，and guides to solve the optimization issue of complex simulated system．