In tandem with social and economic development in Beijing, traffic congestion and the resulting air pollution have become serious problems. To improve the environment as well as road-carrying capacity, this study established a vehicle emission reduction management model using a system dynamics approach. An algorithm for the qualified verification of the degree of grey incidence based on system dynamics and grey model theory was also established to validate the model. Furthermore, in consideration of economic, environmental, social, and health benefits, the effects of the air pollution charging fee(APCF), penalties, and subsidies(collectively, the APS strategy) on air quality and traffic congestion were explored. The findings indicated that APCF and penalties help reduce missions and alleviate traffic congestion but increase the burden on public transport and reduce its supply level. Further, while the subsidy strategy's effects on reducing congestion and emissions are not obvious, the strategy will greatly increase the supply of public transport. In addition, the lagged and fading effects of the combined APS strategy were identified. The combined APS strategy has multiple benefits: it can not only increase public-transport supply and promote health (social and health benefits) but also decrease pollution and total energy consumption (economic and environmental benefits).