Civil aviation is one of the industries facing the greatest challenge in reaching carbon neutrality by the middle of this century, and this sector also contributes to adverse impacts on the regional air quality and human health. China exhibits the second highest air passenger turnover worldwide. Our understanding of civil aviation emissions must be urgently enhanced, and the mitigation potential should be explored. In this study, on the basis of real domestic flight information for 2019, we built a greenhouse gas and air pollution emission inventory for the civil aviation sector in China with the fuel flow method based on the cruise and other phases. We thoroughly analyzed emissions by region, aircraft and engine types, and aircraft age, based on which we designed four measures to evaluate the abatement potential. We found that the hydrocarbon (HC), CO, NOx, SO2, particulate matter (PM) and CO2 emissions in 2019 reached 79.9 kt (95% CI [51.6–114.5]), 176.3 kt (95% CI [114.5–248.2]), 304.2 kt (95% CI [203.4–420.7]), 23.2 kt (95% CI [14.2–33.7]), 1.0 kt (95% CI [0.61–1.44]) and 87.0 Mt (95% CI [57.4–119.6]), respectively. The cruise phase was the major emission phase, accounting for 67%-87% of the total pollutant emissions. If four measures were jointly implemented, the HC, CO, NOx, SO2, PM and CO2 emissions could be reduced by 61%, 54%, 55%, 45%, 32% and 38%, respectively. Utilizing lower-emission aircraft and switching travel modes could substantially reduce civil aviation emissions in China.