Purpose: This study proposed a DEA (Data Envelopment Analysis)-based stepwise benchmarking target selection for inefficient DMU (Decision Making Unit) to improve its efficiency gradually to reach most efficient frontier considering resource (DEA inputs and outputs) improvement preferences. Methods: The proposed method proceeded in two steps. First step evaluates efficiency of DMUs by using DEA, and an evaluated DMU selects benchmarking targets of HCU (Hypothesis Composit Unit) or RU (Real Unit) considering resource improvement preferences. Second step selects stepwise benchmarking targets of the inefficient DMU. To achieve this, this study developed a new DEA model, which can select a benchmarking target of an inefficient DMU in considering inputs or outputs improvement preference, and suggested an algorithm, which can select stepwise benchmarking targets of the inefficient DMU. Results: The proposed method was applied to 34 international ports for validation. In efficiency evaluation, five ports was evaluated as most efficient port, and the remaining 29 ports was evaluated as relative inefficient port. When port 34 was supposed as evaluated DMU, its can select its four stepwise benchmarking targets in assigning the preference weight to inputs (berth length, total area of pier, CFS, number of loading machine) as (0.82, 1.00, 0.41, 0.00). Conclusion: For the validation of the proposed method, it applied to the 34 major ports around the world and selected stepwise benchmarking targets for an inefficient port to improve its efficiency gradually. We can say that the proposed method enables for inefficient DMU to establish more effective and practical benchmarking strategy than the conventional DEA because it considers the resource (inputs or outputs) improvement preference in selecting benchmarking targets gradually.