Ship emissions contribute significantly to air pollution and pose health risks to residents of coastal areas in China, but the current research remains incomplete and coarse due to data availability and inaccuracy in estimation methods. In this study, an integrated approach based on the Automatic Identification System (AIS) was developed to address this problem. This approach utilized detailed information from AIS and cargo turnover and the vessel calling number information and is thereby capable of quantifying sectoral contributions by fuel types and emissions from ports, rivers, coastal traffic and over-the-horizon ship traffic. Based upon the established methodology, ship emissions in China from 2004 to 2013 were estimated, and those to 2040 at 5-year intervals under different control scenarios were projected. Results showed that for the area within 200 nautical miles (Nm) of the Chinese coast, SO2, NOx, CO, PM10, PM2.5, hydrocarbon (HC), black carbon (BC) and organic carbon (OC) emissions in 2013 were 1010, 1443, 118, 107, 87, 67, 29 and 21 kt yr−1, respectively, which doubled over these 10 years. Ship sources contributed ∼ 10 % to the total SO2 and NOx emissions in the coastal provinces of China. Emissions from the proposed Domestic Emission Control Areas (DECAs) within 12 Nm constituted approximately 40 % of the all ship emissions along the Chinese coast, and this percentage would double when the DECA boundary is extended to 100 Nm. Ship emissions in ports accounted for about one-quarter of the total emissions within 200 Nm, within which nearly 80 % of the emissions were concentrated in the top 10 busiest ports of China. SO2 emissions could be reduced by 80 % in 2020 under a 0.5 % global sulfur cap policy. In comparison, a similar reduction of NOx emissions would require significant technological change and would likely take several decades. This study provides solid scientific support for ship emissions control policy making in China. It is suggested to investigate and monitor the emissions from the shipping sector in more detail in the future.