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Currently, air quality has become central to global environmental policymaking. As a typical mountain megacity in the Cheng-Yu region, the air pollution in Chongqing is unique and sensitive. This study aims to comprehensively investigate the long-term annual, seasonal, and monthly variation characteristics of six major pollutants and seven meteorological parameters. The emission distribution of major pollutants is also discussed. The relationship between pollutants and the multi-scale meteorological conditions was explored. The results indicate that particulate matter (PM), SO 2 and NO 2 showed a “U-shaped” variation, while O 3 showed an “inverted U-shaped” seasonal variation. Industrial emissions accounted for 81.84%, 58% and 80.10% of the total SO 2 , NOx and dust pollution emissions, respectively. The correlation between PM2.5 and PM10 was strong ( R = 0.98). In addition, PM only showed a significant negative correlation with O 3 . On the contrary, PM showed a significant positive correlation with other gaseous pollutants (SO 2 , NO 2 , CO). O 3 is only negatively correlated with relative humidity and atmospheric pressure. These findings provide an accurate and effective countermeasure for the coordinated management of air pollution in Cheng-Yu region and the formulation of the regional carbon peaking roadmap. Furthermore, it can improve the prediction accuracy of air pollution under multi-scale meteorological factors, promote effective emission reduction paths and policies in the region, and provide references for related epidemiological research. Graphical abstract Supplementary Information The online version contains supplementary material available at 10.1007/s11270-023-06279-8.