As the critical components for marine low-speed diesel engine flue gas waste heat recovery (WHR) supercritical carbon dioxide (S-CO2) Brayton cycle system, the structure of the compressor impeller is optimized by the evolutionary algorithm (EA) based on the co-simulation of the CAESES, ANSYS CFX and Opti Slang. The law of impeller pressure ratio, efficiency and power consumption in S-CO2 Brayton cycle (SCBC) as a function of rotational speed, inlet temperature, pressure and impeller structural parameters are revealed, and the method of improving SCBC efficiency for marine low-speed diesel engine flue gas waste heat recovery is studied. The optimized impeller structure is greatly enhanced in aerodynamic performance and safety, and the isentropic efficiency is increased by 2.54%, the pressure ratio is increased by 35.64%, and the temperature rise is increased by only 4.6%. A 100kW S-CO2 compression cycle test bench was set up to verify the simulation-optimized impeller results. The final results show that the optimized impeller structure, aerodynamic performance and safety are greatly improved. It provides theoretical support for selecting and optimising compressor impellers for marine low-speed diesel engine flue gas waste heat recovery S-CO2 Brayton cycle.