Economic growth and globalization have led to a surge in civil aviation transportation demand. Among the major economies in the world, China has experienced a 12-fold increase in terms of total passenger aviation traffic volume since 2000 and is expected to be the largest aviation market soon. To better understand the environmental impacts of China's aviation sector, this study developed a real-world flight trajectory-based emission inventory, which enabled the fine-grained characterization of four-dimensional (time, longitude, latitude, and altitude) emissions of various flight stages. Our results indicated that fuel consumption and CO2 emissions showed two peaks in altitude distribution: below 1,000 m and between 8,000 and 12,000 m. Various pollutants depicted different vertical distributions; for example, nitrogen oxides (NOX) had a higher fraction during the high-altitude cruise stage due to the thermal NOX mechanism, while hydrocarbons had a dominant fraction at the low-altitude stages due to the incomplete combustion under low-load conditions. This improved aviation emission inventory approach identified that total emissions of CO2 and air pollutants from short-distance domestic flights would be significantly underestimated by the conventional great-circle-based approach due to underrepresented calculation parameters (particularly, flight distance, duration, and cruise altitude). Therefore, we suggest that more real-world aviation flight information, especially actual trajectory records, should be utilized to improve assessments of the environmental impacts of aviation.