To characterize the air pollutants in Shanghai Port and identify the contribution from ship traffic emission, field measurements have been conducted in 2011. The trace gases SO2, NO2 and O3 were monitored and aerosol samples of TSP, PM2.5 and size-segregated particles were collected in a working area of Shanghai Port. Elements including V, Ni, Al, Fe, Si, Ca, Na, Mg, Mn, Zn, Co, Cr in aerosol samples and heavy fuel oil samples were analyzed. The results revealed that average hourly SO2 and NO2 concentrations in Shanghai Port were respectively 29.4 and 63.7 μg m−3, average daily concentrations of TSP and PM2.5 were 114.39 and 62.60 μg m−3, comparable with the ones in Shanghai land area. Ni and V were found enriched in fine particles with averaged concentrations of 80.0 and 14.8 ng m−3 in PM2.5 respectively. Also ratio of V/Ni in aerosol under summertime airflow was 3.4, very close to the ratio of averaged V and Ni content in international heavy fuel oils used in Shanghai Port. The backward trajectory analysis further revealed that SO2, NO2, and V under coastal airflows were mainly from ship traffic emission. The mean concentration of V was 15.84 ng m−3 under hybrid coastal airflows, much higher than that of 9.84 ng m−3 under continental airflows. Furthermore, V was found to be highly correlated with ship fluxes, and was selected as an indicator of ship traffic emission in Shanghai. The estimated primary PM2.5 contribution from ship traffic ranged from 0.63 to 3.58 μg m−3, with an average of 1.96 μg m−3. This PM2.5 fraction accounted for 4.23% of the total PM2.5 in an average level, and reached to a maximum of 12.8%. Furthermore, there could be 64% of primary PM2.5 contributed by ships in Shanghai Port transported to inland region. Our results suggest that ship traffic has a non-negligible contribution on ambient levels of fine particles and secondary contribution of SO2 and NO2 emitted by ships need to be estimated on local and regional scale in future.