The city clusters in eastern coastal China have suffered from serious air pollution in the past decades, which is partially related to the complex local topography and meteorological conditions. The planetary boundary layer (PBL) scheme is a critical parameter for accurate meteorology simulations and air quality predictions. In this study, we analyze the impact of four typical PBL schemes, namely, Yonsei University (YSU), Mellor-Yamada-Nakanishi-Niino Level 2.5 (MYNN), Asymmetric Convective Model version 2 (ACM2), and Mellor-Yamada-Janjic (MYJ) PBL, within the Weather Research and Forecasting (WRF) model to assess their impacts on the simulations of air pollutant concentrations based on the Comprehensive Air Quality Model with Extensions (CAMx) for the Yangtze River Delta (YRD) region, one of the most developed city clusters in eastern China. The results indicate that the MYNN scheme performs best in terms of fine particulate matter (PM2.5) and nitrogen dioxide (NO2) simulations, with mean bias of 4.8 μg m−3 and 9.3 μg m−3 in summer and 11.7 μg m−3 and 5.4 μg m−3 in winter, respectively. The YSU scheme performs best for ozone (O3) prediction, with better simulation results in summer than in winter. Notably, some discrepancies among different PBL schemes in the prediction of air pollution are directly associated with the complex topography. For the prediction of PM2.5, the MYJ and YSU schemes tend to overestimate the concentrations in the plains of Jiangsu and northern Anhui while underestimating PM2.5 in the hilly areas compared with the MYNN scheme. Meanwhile, the performance of the ACM2 scheme is opposite to that of the MYJ and YSU schemes. For O3 predictions, MYJ overestimates O3 in the eastern coastal area and underestimates O3 in the inland areas in summer compared with the YSU scheme, while the ACM2 scheme is the opposite of the MYJ scheme, and the MYNN scheme consistently overestimates O3.