China has a large number of trucks, railway freight locomotives, water transport ships, and cargo planes, with a huge amount of freight turnover. The consumption of fossil fuels has resulted in significant emissions of CO2 and air pollutants from China’s freight transportation sector. This study constructed a China-Freight-Transport CIMS model, based on the implementation of global carbon tax policies and China’s carbon price level, set different carbon tax rates scenarios, and conducted simulation analysis. The simulation results showed that with the continuous growth of China’s freight scale, the carbon tax policy can reduce the proportion of diesel trucks, fuel oil ships, etc., while promoting the application of electric trucks and hydrogen fuel trucks. Compared with the business as usual scenario, under the carbon tax scenarios, the emissions amount and the emission intensity of CO2 and air pollutants had decreased, which helped to reduce the peak level of CO2 emissions in China’s freight transportation sector.