The rapid growth of urbanization in China has led to a substantial escalation in the demand for civil aviation services, consequently propelling China to the third-largest contributor of carbon emissions within the aviation sector. Using the 2012–2021 data on takeoffs and landings of civil aviation aircraft in China, the aircraft engine emission factor database of the Base of Aircraft Data (BADA) from EUROCONTROL, this paper investigates the spatial-temporal distribution characteristics of atmospheric pollutants, primarily carbon emissions from Chinese civil aviation aircraft in 19 megacities. The results indicate that (1) China’s aviation CO2 emissions equivalent between 2012 and 2022 has been on an upward trajectory, peaking at 186.53 MT in 2019 with an average annual growth of 12.52%. The trend, albeit momentarily interrupted by the COVID-19 pandemic, appears to persist. (2) CO2 constitutes the highest proportion of aircraft emissions at 83.87%, with Cruise Climb Descent (CCD) cycle emissions accounting for 96.24%. CO2 and NOX, with the highest increase rates in the CCD and Landing and Takeoff (LTO) phases, respectively, are identified as the chief culprits in aviation-related greenhouse effects. (3) There is a marked spatial imbalance, with 19 megacities contributing 62.08% of total CO2 emissions, compared to the 207 least-emitting cities contributing just 9.29%. (4) The pattern of city carbon emissions is changing, with rapid growth rates in the western cities of Xinjiang, Tibet, Shaanxi, and Guizhou, and varied growth rates among megacities. The implications of this study emphasize the urgency for advancements in aviation fuel technology, rigorous management of CCD phase pollutants, strategic carbon emission controls in populous cities, fostering green aviation initiatives in western regions, diverse carbon mitigation tactics, and strengthening the precision and surveillance of aviation carbon accounting systems. Collectively, this study paints a grand picture of the complexities and challenges associated with China’s urban sprawl and aviation carbon emissions.