The huge fuel consumption of shipping activities has a great impact on the ecological environment, port city environment, air quality, and residents’ health. This paper uses Automatic Identification System (AIS) data records and ship-related data in 2021 coastal waters of the United States to calculate pollutant emissions from ships in 30 ports of the United States in 2021. After calculating the pollutant emissions from ships at each port, the multiscale geographically weighted regression (MGWR) model is used to analyze the factors affecting the ship pollutant emissions. Geographically weighted regression (GWR) model is used to investigate the spatial heterogeneity of various factors affecting the characteristics of ship pollutant emissions at different scales. This paper mainly compares the effect of models of GWR and MGWR. MGWR may truly reveal the scale difference between different variables. While controlling the social and economic attributes, the coastline length, container throughput, and population are used to describe the spatial effects of ship pollutant emissions in the United States. The results denote that the distribution trend of ship pollutant emissions has a gap based on various ship types and ports. NOx accounts for the highest proportion of pollutant emissions from port ships, followed by SO₂ and CO. The impact coefficients of coastline length and population on pollutant emissions in port areas are mostly positive, indicating that the growth of coastline length and population will increase pollutant emissions in port areas, while the effect of container throughput is opposite. Relevant departments should put forward effective measures to curb NOx emission. Port managers should reasonably plan the number of ship transactions according to the coastline length of the port.