Air pollution has worsened as a result of increased traffic congestion in cities. Using air pollution caused by motor vehicle emissions (mainly by carbon monoxide, hydrocarbon, nitrogen oxide, and particulate matter) as an example, in this study, we applied an integrated algorithm comprising system dynamics, entropy weight method, and gray system theory to establish a weighted logic function. A vehicle pollutant control model (including the transport, health, and environmental subsystems) was established by VENSIM software. The medium- and long-term key variable analysis showed that the integrated algorithm, fully reflecting the advantages of system dynamics and gray system theory, more accurately described air pollution caused by vehicle emissions. Our research results also revealed that the combined strategy of penalties and air pollution charging fee had a threefold effect: reduced congestion and emissions, improved health impact index, and reduced number of illegal trips. Specifically, the degree of traffic congestion, number of illegal trips, and the degree of air pollution decreased by approximately 82.40%, 69.35%, and 68.91%, respectively, whereas the health impact index increased by about 279.03%. This finding provides guidance for improving policy and optimizing management and control modes.