Civil aviation transport is a key area of fossil energy consumption and greenhouse gas emission, and it is also an important source of air pollutants; the emissions of these have caused severe environmental problems. In this paper, we estimated the emissions in 235 domestic civil airports, and predicted the future trends of CO2 and air pollutant emissions from civil aviation in China until 2050 under three scenarios. The co-reduced emissions of each measure were evaluated by using the co-control effects coordinate system. The results show that in 2018, the emissions of CO2, NOx, SO2, CO, PM and HC were 117.23 × 106 tons, 90.47 × 104 tons, 14.37 × 104 tons, 9 × 104 tons, 1.29 × 104 tons and 0.66 × 104 tons, respectively. CO2, NOx, SO2 and PM emissions were mainly concentrated in cruise mode, accounting for 87–93% of the total emissions; HC and CO emissions were more frequently from the LTO. Under the baseline scenario, the growth rate of air pollutant emissions will account for a greater share, from 84% in 2030 to 464% in 2050, whereas the general scenario reduces emissions by 15% and 71%, respectively, and a higher reduction of 26% and 93% is seen in the stringent scenario. Improving aviation fuels is the most significant co-reduction measure, which can reduce CO2 by 89% and 68% in 2030 and 2050, and reduce air pollutants by 86–89% and 62–65%, respectively.