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In a cross-docking system, trucks must be scheduled to minimize the total flow time of the system. This problem is NP-hard, and this study proposes two hybrid meta-heuristics—hybrid simulated annealing and hybrid variable neighborhood search—to solve it by achieving the best sequence of truck pairs. The Taguchi method serves to reveal the best robustness of these algorithms. To demonstrate the effectiveness of the proposed methods, especially for large-sized problems, this study solves various test problems, and the computational results clearly reveal that the proposed methods outperform previous approaches.