Marine engines often use diesel as an alternative fuel to improve the economy. In recent years, waste oil, biodiesel and alcohol fuel are the most famous research directions among the alternative fuels for diesel. With the rapid development of the shipping industry, the air of coastal areas is becoming increasingly polluted. It is now necessary to reduce the emission of marine engines to meet the strict emission regulations. There are many types of alternative fuels for diesel oil and the difference of the fuel may interfere with the engine emissions; however, PM, HC, CO and other emissions will have a negative impact on SCR catalyst. This paper reviews the alternative fuels such as alcohols, waste oils, biodiesel made from vegetable oil and animal oil, and then summarizes and analyzes the influence of different alternative fuels on engine emissions and pollutant formation mechanism. In addition, this paper also summarizes the methods that can effectively reduce the emissions of marine engines; it can provide a reference for the study of diesel alternative fuel and the reduction of marine engine emissions.