Evaluation of models for simulating temporal and spatial variations of PM2.5 chemical composition in Japan has been limited by the lack of observational data. In this study, we used PM2.5 chemical composition data measured simultaneously over several regions of Japan in winter, spring, and summer 2012 to evaluate three sensitivity simulations, one based on a secondary organic aerosol (SOA) yield model and two based on a volatility basis set (VBS) model. Concentrations of sulfate (SO42–), nitrate (NO3–), and ammonium (NH4+) were well reproduced by all the simulations in summer. However, in winter and spring, SO42– concentrations were underestimated and NO3– concentrations were overestimated by the standard simulation. NO3– concentrations were better reproduced by a model with dry-deposition velocities of nitric acid and ammonia enhanced by a factor of 5, as was done in a previous study. Observed concentrations of elemental carbon and organic aerosol (OA) were higher at urban sites than at the surrounding remote sites, and this behavior was not adequately reproduced by models with a grid size of 15 km. Further refinements of emission inventories and models are necessary for better simulations of PM2.5 chemical compositions. OA concentration was greatly underestimated by the simulation based on the SOA yield model over all the seasons but was better reproduced by the simulations based on the VBS model in spring and summer because aging reactions were considered in the VBS model-based simulations. The VBS model-based simulations reproduced the observations that primary OA predominated in winter and that the contribution of SOA was higher than that of primary OA in spring and summer. These contributions should be validated by means of observation-based source contributions of OA in future studies.