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This study intended to optimize the favorable operating conditions for Bench-scale shipboard STP by using artificial wastewater. For this purpose, the previously developed advanced sequence batch reactor and membrane bioreactor (MBR) combined system by our group was adopted at Bench-scale to study the applicability of this system for wastewater treatment and for the removal of nutrient and organic matter. The COD:T-N:T-P ratios of the influent were adjusted at 10:3:1 and the aeration during MBR process was provided at 7 min aeration and 3 min stop. The operating conditions were optimized by measuring the removal efficiencies of CODcr, T-P, and T-N at different time intervals of mixing and aeration. The operating conditions included mixing and aeration for 90:30, 80:40, 70:50, and 60:60 min, respectively. The optimal removal efficiencies were achieved under mixing and aeration for 70 min and 50 min, respectively, using Bench-scale shipboard STP. The results of the present study were in accordance with the MEPC.227(64) regulations for the removal of CODcr, phosphorus, and nitrogen for advanced shipboard wastewater treatment. A further study is required to evaluate a detailed mechanism of shipboard STP to justify the MEPC.227(64) regulations.