This study adopts 25 kHz ultrasonic wave and 0.4T magnetization field in online optimization of Marine Heavy Fuel Oil (MHFO). It aims at studying the feasibility of optimizing the combustion and emission performance of two-stroke marine diesel engine with one kind of MHFO with ultrasonic wave and magnetization field. The results show that engine's fuel consumption could reach 222 g/kW center dot h under 25% of engine rated power, while this consumption reduces to 188 g/kW center dot h under 90% of engine rated power. It can be seen that the rate of fuel consumption decreased by about 15% between 25% and 90% of engine rated power. The improved combustion performance under high operating load conditions produced low carbon monoxide (CO) and carbon dioxide (CO2) emissions. The rise of in-cylinder temperature promoted the formation of nitrogen oxides (NOx), in which nitrogen oxide (NO) accounted for about 99.5% of the NOx composition. Through the optimization of online MHFO with ultrasonic waves and magnetization field device under 25% of engine rated power, the engine's fuel consumption rate decreased by about 1.5%. This shows that CO and CO2 emissions have been effectively reduced. However, the NOx emissions increased slightly. The CO, CO2 and NOx emissions decreased when the engine's power increased form 50% to 75%, In this operating range, its fuel saving decreased from 0.4% to 0.08%. At 90% of engine rated power the volume concentration of CO emissions and fuel consumption rate increased. However, its CO2 emissions decreased, while the NOx emissions remained unchanged.