The planetary boundary layer (PBL) structure and its evolution can significantly affect air pollution. Here, the PBL’s characteristics and their association with air pollution were analyzed in Hefei, east China, using ERA5 reanalysis data, weather observations and air pollutant measurements from 2016 to 2021. In the near-surface level, air pollution was directly influenced by ground meteorological conditions, and high PM2.5 was normally related to weak wind speed, northwest wind anomalies, low temperature and high relative humidity. Moreover, in the trajectory analysis, air masses from the north and the northwest with short length played an important role in the high PM2.5 with pollutant transport within the PBL. Furthermore, high PM2.5 showed a tight dependence on PBL stratification. There was high temperature and relative humidity and low wind speed and PBL height within all PBL altitudes in the polluted condition. Notably, vertical wind shear (VWS) and temperature gradient tended to be much weaker below 900 hPa, which created a deeply stable stratification that acted as a cap to upward-moving air. Such a PBL structure facilitated more stable stratification and enhanced the generation of air pollution. Finally, the stable stratification in the PBL was related to the special synoptic configuration for the high PM2.5 conditions, which included the block situation at the high level, the southerly wind anomalies at the middle level and the wild range of the uniform pressure field at the near-ground level. Therefore, air pollutant concentrations were regulated by ground factors, PBL structure and the synoptic situation. Our results provide a precise understanding of the role of PBL features in air pollution, which contributes to improving the assimilation method of the atmospheric chemistry model in east China.