The key of realizing the cross docking is to design the joint of inbound trucks and outbound trucks, so a proper sequence of trucks will make the cross-docking system much more efficient and need less makespan. A cross-docking system is proposed with multiple receiving and shipping dock doors. The objective is to find the best door assignments and the sequences of trucks in the principle of products distribution to minimize the total makespan of cross docking. To solve the problem that is regarded as a mixed integer linear programming (MILP) model, three metaheuristics, namely, harmony search (HS), improved harmony search (IHS), and genetic algorithm (GA), are proposed. Furthermore, the fixed parameters are optimized by Taguchi experiments to improve the accuracy of solutions further. Finally, several numerical examples are put forward to evaluate the performances of proposed algorithms.