To characterize the concentrations of CO<sub>2</sub> and CH<sub>4</sub> in the urban atmospheric boundary layer (ABL), this study conducted airborne measurements over four cities in Eastern China, obtaining full vertical profiles (ground to 2 km) over Beijing and Nanjing, partial profiles over Hengshiu and Shangqiu. Results showed that the CO<sub>2</sub> and CH<sub>4</sub> concentrations in the ABL were consistently higher than those in the free atmosphere, with the highest values observed near the surface (Beijing and Nanjing). In Beijing, the daytime and nighttime inversion jumps in the CO<sub>2</sub> concentration were −25.2 ppm and −18.0 ppm, respectively. In Nanjing, the corresponding values were −9.5 ppm and −10.0 ppm. For CH<sub>4</sub>, the inversion jumps were −171 ppb during the day and −203 ppb at night (Beijing); in Nanjing, they were −141 ppb and −108 ppb, respectively. Change in the airmass trajectory altered the free-atmospheric CO<sub>2</sub> concentration over Nanjing by 3 ppm in a matter of a few hours. The CH<sub>4</sub>:CO<sub>2</sub><sub> </sub>emissions ratio inferred from the nighttime ABL concentration data was lower than that obtained from the EDGAR inventory by 17 % in Beijing and 82 % in Nanjing, indicating that the inventory may have missed the recent energy transition from gasoline and natural gas to electric in the transport sector. The experimental data is available at <a href="https://doi.org/10.7910/DVN/ZPVSVU" target="_blank" rel="noopener">https://doi.org/10.7910/DVN/ZPVSVU</a>.