Air pollution caused by ship exhaust emission is receiving more and more attention. The physical and chemical properties of fuels, such as sulfur content and PAHs content, potentially had a significant influence on air pollutant emissions from inland vessels. In order to investigate the effects of fuel qualities on atmospheric pollutant emissions systematically, a series of experiments was conducted based on the method of actual ship testing. As a result, SO2, PM and NOx emission rates all increased with the increase of main engine rotating speed under cruise mode, while PM and NOx emission factors were inversely proportional to the main engine rotating speed. Moreover, SO2 emission factor changed little with the increase of the main engine rotating speed. In summary, the fuel-dependent specific emission of SO2 was a direct reflection of the sulfur content in fuel. The PM emission increased with the increase of sulfur content and PAHs content in fuel. However, fuel qualities impacted little on NOx emissions from inland vessels because of NOx formation mechanisms and conditions. Implications: Ship activity is considered to be the third largest source of air pollution in China. In particular, air pollutants emitted from ships in river ports and waterways have a direct impact on regional air quality and pose threat on the health of local residents owing to high pollutants concentration and poor air diffusion. The study on the relationship between air pollutant emissions and fuel quality of inland vessels can provide foundational data for local authority to formulate reasonable and appropriate policies for reducing atmospheric pollution due to inland vessels.