The vehicle portable emission measurement system (PEMS) was used to study the pollutant emission from harbor machinery in Qingdao Port. The emission characteristics of different types of harbor machinery were summarized under different conditions, and the emission factors of harbor machinery were calculated. The results showed that emission rate of harbor machinery under working condition was 1.34~2.66 times higher than that under idle condition. When the harbor machinery power was higher than 130kW, the emission rates climbed to 4.18~41.56 times. For high-power harbor machinery, emission status under idle condition could hardly reflect the actual emissions rates under working condition. Based on the analysis of fuel-based emission factors, the trend of CO, THC and NO_x emission factors were consistent under three conditions. The PM emission factors reflected different characteristics. PM emission factors under working conditions were 10 times higher than that under idle conditions. When the service time exceeded 4500 hours, the pollutant emission significantly increased, especially for forklift trucks, which was 1.64~8.25 times higher than before. The actual emission level of harbor machinery was 1.5~2 times higher than the average level of non-road machinery. It could be found that the difference of CO, THC and PM emission levels among different emission standards was 1.73~5.38 times using two-idle speed method, but the level of NO_x emission was too close and undistinguishable.