Accurate air pollutant prediction is essential for addressing environmental and public health concerns. Air quality models like WRF-CMAQ provide simulations, but often show significant errors compared to observed concentrations. To identify the sources of these model biases, we applied the XGBoost machine learning algorithm to assess the performance of WRF-CMAQ in predicting air pollutants across two regions in China. XGBoost models trained with observations achieved high accuracy (R > 0.95), indicating that the selected features effectively capture pollutant variations. When trained on WRF-CMAQ inputs, XGBoost still improved performance but revealed biases linked to both model inputs (10–60%) and mechanisms (1–30%). Analysis identified previous-hour pollutant levels as the largest bias contributor, followed by meteorological variables. The study highlights the need for improving both model inputs and mechanisms to enhance future air quality predictions and support pollution control strategies.