In recent years, marine auxiliary diesel engine has been widely used to produce electricity in the large ocean-going ship. One of the main technical challenges for ocean-going ship is to reduce pollutant emissions from marine auxiliary diesel engine and to meet the criteria of disposal on ships pollutants of IMO (International Maritime Organization). Different technical changes have been introduced in marine auxiliary diesel engine to apply clean fuels to reduce pollutant emissions. The ultralow sulfur light fuel will be applied in diesel engine for emission reductions in China. This study is aimed to investigate the impact of fuel (ultralow sulfur light fuel) on the combustion characteristic, NOx and green house gas emissions in a marine auxiliary diesel engine, under the 50%-90% engine speeds and the 25%-100% engine torques. The experimental results show that, in the marine auxiliary diesel engine, the cylinder pressure and peak heat release rate increase slightly with the increase of engine torques, while the ignition advances and combustion duration become longer. With the increases of the engine speed and torque, the fuel consumption decreases significantly, while the temperature of the exhaust manifold increases. The NOx emissions increase significantly with the increases of the engine speed and torque. The NO emission increases with the increases of the engine speed and torque, while the NO2 emission decreases. Meanwhile, the ratio of NO2 and NO is about 1:1 when the diesel engine operated in the low speed and load, while the ratio increases significantly with the increases of engine speed and torque, due to the increase of the cylinder temperature in the diffusive combustion mode. Moreover, the CO2 emission increases with the increases of engine speed and torque by the use of ultralow sulfur light fuel.