Many Firms consider the application of a cross-docking system to reduce inventory and lead-time. However, most studies mainly concentrate on the design of a cross-docking system. This study presents the method that selects the cross-docking center under the existing logistics network. Describing the operation environment to apply the cross-docking system, the selection criteria of the cross-docking center, and the main constraints of transportation planning under the environment of multi-level logistics network, we define the selection problem of the cross-docking center applied to a logistics field. We also define the simulation model that can analyze variously the cross-docking volume and develop the selection methodology of the cross-docking center. The simulation model presents the algorithm and influence factors of the cross-docking system, the decision criteria of the system, policy parameter, and input data. In addition, this study analyzes the effect of increasing the number of simultaneous receiving and shipping docks, and the efficiency of the overnight transportation and cross-docking by evaluating each scenario after simulating the scenarios with the practical data of the logistics field.