The influence of gas intake temperature, composition and the volume concentration of each gas component on diesel engine combustion, emission and the output power was studied by building a calculation model of the B&W 6S35ME-B9 marine two-stroke low-speed diesel engine, followed by a comprehensive optimization exploration. The results showed that under 295 K and 18.5% O2 of intake gas, the engine’s NOx emission is only 4.5 g/kWh and reduced to 58% from the normal air gas intake condition. Moreover, their power output is very similar. In addition, the effect of CO2 or H2O added into the intake of the diesel engine on the performance of the diesel engine can be compensated by reducing the intake temperature. At the intake temperature of 295 K, the engine’s NOx emission with 20.58% O2, 77.42% N2 and 2% H2O is 8.62 g/kWh, and 9.06 g/kWh under 20.79% O2, 78.21% N2 and 2% CO2. It is lower than 11.77 g/kWh, which is under normal intake conditions (315 K, 21%O2 and 79%N2). The power output is also similar to the normal intake condition. Therefore, the comprehensive optimization of gas intake temperature, composition and concentration can effectively optimize the diesel engine’s performance in terms of combustion, emission and power output. The research results have an important reference value for the optimization of diesel engine performance.