Ship emissions have the potential to contribute to air quality degradation in port cities. In this study, PM2.5 samples from two sites with different distance away from the chipping channel of Xiamen Port in Southeastern China between November 2015 and May 2018 were collected and subjected to chemical analysis such as water soluble ions, carbonaceous components and elements. The annual average PM2.5 mass concentrations were 55.8 ± 22.7 µg m-3 and 56.5 ± 24.5 µg m-3 at the urban and suburban sites, respectively, with the lowest values in summer and the highest in winter/spring. Significantly higher values for vanadium (V) and nickel (Ni) were found at the urban site due to the short distance between the site and shipping channel. Using a PMF model, six source factors were identified: sulfate and ship emissions (16.6–20.9%), secondary nitrate and chloride (14.7–17.3%), fugitive dust (16.9–23.0%), industrial emissions (5.5–7.0%), primary organic aerosol (14.1–14.8%), and traffic emissions and biomass burning (23.8–24.6%). Potential source contribution function analysis indicated that air masses from the South China Sea contributed significantly to the ship emissions source. The PMF-based method did not separate ship primary emissions from secondary sulfate. When a V-based method was used, the primary PM2.5 from ship emissions plus its associated secondary sulfate was shown to contribute 5.5–8.9% of the ambient PM2.5 on average. The results from the V-based method exhibited strong positive correlations with those of PMF-based method. Considering the potential negative effect on the air quality and the expanding international maritime trade in the long term, these results indicate that policies and regulations for the control of ship emissions are required in all major port cities, not just those in the domestic emission control areas of China.