The transport sector has become an important source of urban greenhouse gas (GHG) and air pollutant emissions, with the continuous growth of transportation demand. The co-benefits of reducing GHG and air pollutant emissions in the transport sector are receiving more and more attention. Taking Guangzhou as the case study city, this study quantitatively analyzed the co-benefits of reducing CO2 and air pollutant emissions under the sustainable scenario in the transport sector by developing a quantitative analysis model based on the Long-range Energy Alternatives Planning (LEAP) framework. The co-benefits quantitative parameter and the co-benefits radar chart analysis method are used to identify and evaluate the generated co-benefits, and then the co-benefits generated by implementing the sustainable measures are discussed. The results show that adjusting transport modes and increasing the application of electricity are the two most effective measures for achieving the co-benefits of reducing CO2 and air pollutant emissions in the Guangzhou transport sector. Thus, these two measures are highly preferential for mitigating CO2 and air pollutant emissions. In addition, increasing the application of biofuel and hydrogen energy also has good co-benefits. However, increasing the application of Liquefied Natural Gas (LNG) has poor co-benefits. Promoting the utilization of LNG intercity buses, trucks, and cargo ships will lead to emission increases of CO and HC compared to the current policy scenario, and small emission reductions of CO2 and other air pollutants. Therefore, to promote the utilization of LNG vehicles and ships, it is necessary to cooperate with the use of air pollutant end removal devices and high-pressure direct injection (HPDI) gas engines.