Accurate exposure estimates are required for health effect analyses of severe air pollution in China. Chemical transport models (CTMs) are widely used to provide spatial distribution, chemical composition, particle size fractions, and source origins of air pollutants. The accuracy of air quality predictions in China is greatly affected by the uncertainties of emission inventories. The Community Multiscale Air Quality (CMAQ) model with meteorological inputs from the Weather Research and Forecasting (WRF) model were used in this study to simulate air pollutants in China in 2013. Four simulations were conducted with four different anthropogenic emission inventories, including the Multi-resolution Emission Inventory for China (MEIC), the Emission Inventory for China by School of Environment at Tsinghua University (SOE), the Emissions Database for Global Atmospheric Research (EDGAR), and the Regional Emission inventory in Asia version 2 (REAS2). Model performance of each simulation was evaluated against available observation data from 422 sites in 60 cities across China. Model predictions of O₃ and PM_2.5 generally meet the model performance criteria, but performance differences exist in different regions, for different pollutants, and among inventories. Ensemble predictions were calculated by linearly combining the results from different inventories to minimize the sum of the squared errors between the ensemble results and the observations in all cities. The ensemble concentrations show improved agreement with observations in most cities. The mean fractional bias (MFB) and mean fractional errors (MFEs) of the ensemble annual PM_2.5 in the 60 cities are −0.11 and 0.24, respectively, which are better than the MFB (−0.25 to −0.16) and MFE (0.26–0.31) of individual simulations. The ensemble annual daily maximum 1 h O₃ (O₃-1h) concentrations are also improved, with mean normalized bias (MNB) of 0.03 and mean normalized errors (MNE) of 0.14, compared to MNB of 0.06–0.19 and MNE of 0.16–0.22 of the individual predictions. The ensemble predictions agree better with observations with daily, monthly, and annual averaging times in all regions of China for both PM_2.5 and O₃-1h. The study demonstrates that ensemble predictions from combining predictions from individual emission inventories can improve the accuracy of predicted temporal and spatial distributions of air pollutants. This study is the first ensemble model study in China using multiple emission inventories, and the results are publicly available for future health effect studies.