Vehicular emissions have become one of the important sources of air pollution, and their effective control is essential to protect the environment. The Chengdu-Chongqing Urban Agglomeration (CCUA), a less developed area located in the southwest of China with higher vehicle population and special topographic features, was selected as the research area. The aims of this study were to establish multi-year vehicular emission inventories for ten important air pollutants in this area and to analyze emission control policy scenarios based on the inventories. The results showed that the ten vehicular pollutant emissions had differences during the past decade, and CO2 and NH3 increased markedly between 1999 and 2015. Chengdu and Chongqing were the dominant contributors of vehicular emissions in the CCUA. Eight scenarios based on these inventories were designed and the alternative energy replacement scenario was studied from the life-cycle perspective. Compared with the business as usual scenario, elimination of substandard vehicles scenario is the most effective policy to control NOx, PM2.5, PM10, and CH4 emissions; the radical alternative energy replacement scenario could decrease the vehicular NMVOC, CO2, N2O, and NH3 emissions; the elimination of motorcycles scenario could decrease the vehicular CO emissions; and the raising fuel standards scenario could reduce vehicular SO2 emissions significantly (by 94.81%). The radical integrated scenario (combining all of the reduction control measures mentioned above) would achieve the maximum emission reduction of vehicular pollutants CO, NMVOC, NOx, PM2.5, PM10, CO2, N2O, and NH3 compared with any scenario alone.