The aims of this study were to determine compartmental air pollution during navigation of a large oceangoing ship and to identify preliminarily the major pollution sources. During the voyage of a bulk carrier ship, air samples were collected at 18 selected sites using a stratified sampling method. The concentrations of 15 pollutants were determined using gas chromatography. Results showed the concentrations of these pollutants varied significantly among the sampling sites, indicating major pollution sources at or nearby those locations. Five common factors extracted using factor analysis explained 89.092% of the total variance. Multivariate linear regression analysis showed the contributions to air pollution of these five common factors, i.e., the volatilization of ship paint, volatilization of ship-based oil, cooking activities, high-temperature release of rubber components on the ship and daily use of chemical products, and the application of deodorant and insecticide, were 41.07%, 25.14%, 14.37%, 11.78%, and 7.63%, respectively. Three significant groups were determined using cluster analysis based on their similarity, i.e., high, medium, and low pollution of sampling sites. This study established that the air of the bulk carrier ship was heavily polluted, and that effective identification of pollution sources could provide a scientific basis for its control.