Vessel-source air pollution may have a major impact on human health and the marine environment. In this study, a method based on vessel activity intensity was adopted to estimate the emission of air pollutants generated by the consumption of fuel oils from merchant vessels in the Port of Kaohsiung. The vessel activities were determined by using the vessel automatic identification system (AIS) to track vessel traffic and position and to calculate the corresponding emission of air pollutants. It was found that container ships, bulk carriers, and oil tankers, emitted approximately 90% of the total air pollutants. The emissions of SO2 and NOx accounted for 43% and 23%, respectively, when compared to the land-based source emission from the city of Kaohsiung. Management strategies were explored that market-based tools are recommended for the mitigation of vessel-source air pollution along with mandatory utilization of low sulfur fuels.