In order to accurately assess China’s port air pollution caused by AHTS (Anchor Handling Tug Supply Vessels) ships, 46 diesel engines on 27 AHTS ships were tested for onboard emissions using a large gas analyzer to statistically analyze their fuel-based and power-based emission factors. The results show that fuel-based NOx-emission factors for MEs, SEs and AEs before and after the use of the SCR system are 45.4, 38.24,33.04 g/kg and 6.35, 4.98, 5.82 g/kg, CO-emission factors are 7.95, 6.30, 7.96 g/kg and 6.90, 6.93, 8.32 g/kg, THC-emission factors are 0.49, 0.64, 0.25 g/kg and 0.42, 0.47, 0.22 g/kg, and CO2-emission factors are 3121.62, 3121.34, 3093.12 g/kg and 3088.14,3091.40, 3085.21 g/kg, respectively. Power-based NOx-emission factors for MEs, SEs and AEs before and after the use of the SCR system are 9.71, 8.61, 7.58 g/(kW·h) and 1.37, 1.23, 1.33 g/(kW·h), CO-emission factors are 1.71, 2.08, 1.84 g/(kW·h) and 1.47, 1.53, 1.93 g/(kW·h), THC-emission factors are 0.10, 0.14, 0.05 g/(kW·h) and 0.09, 0.13, 0.06 g/(kW·h), and CO2-emission factors are 671.73, 700.58, 718.46 g/(kW·h) and 664.42, 694.16, 716.92 g/(kW·h), respectively. The power-based emission factor is closely related to the diesel engine load, and the relationship between different exhaust emissions and diesel engine load shows different patterns. In addition, it was found that the NOx emissions of the ship decreased significantly to meet the IMO Tier III requirements after running SCR. The emission factors of CO, HC and CO2 have no obvious change whether SCR systems were operated or not. The AHTS marine engine emission factors obtained in this paper are highly relevant and can provide reliable data for establishing a suitable emission inventory for medium and high speed engineering support vessels.