With the same sources of basic data, two emission inventories of on-road mobile source for Jiangsu in 2012 were established based on COPERT and emission factors method respectively. Comparing the two methods, we found that the different applications of emission factors contributed to the big gap of NOX, PM2.5, BC and OC, emission factors method were 2.38, 1.39, 1.49, 2.66, 3.33 and 1.72 times of COPERT respectively. COPERT may underestimate the emission factors of CO, NOX and NMVOC while the uncertainty of emission factors of particular based on observation was larger showed by comparing different monitoring data and COPERT. Passenger car contribute 36% and 23% respectively for CO and NMVOC while the contribution of heavy-duty-truck for NOX, PM2.5 and BC were more than 50%. Based on COPERT and road network information, GIS technology was applied to analyze the spatial distribution of vehicle emission intensity. The results revealed that the contribution of the south of Jiangsu was relative bigger and emission intensity was larger; Moreover, inter-city highway system have a significant impact on the emission distribution of NOX and particular matter.