Satellite-based models for estimating concentrations of particulate matter with an aerodynamic diameter less than 2.5 μm (PM2.5) have seldom been developed in islands with complex topography over the monsoon area, where the transport of PM2.5 is influenced by both the synoptic-scale winds and local-scale circulations compared with the continental regions. We validated Multi-Angle Implementation of Atmospheric Correction (MAIAC) aerosol optical depth (AOD) with ground observations in Japan and developed a 1-km-resolution national-scale model between 2011 and 2016 to estimate daily PM2.5 concentrations. A two-stage random forest model integrating MAIAC AOD with meteorological variables and land use data was applied to develop the model. The first-stage random forest model was used to impute the missing AOD values. The second-stage random forest model was then utilised to estimate ground PM2.5 concentrations. Ten-fold cross-validation was performed to evaluate the model performance. There was good consistency between MAIAC AOD and ground truth in Japan (correlation coefficient = 0.82 and 74.62% of data falling within the expected error). For model training, the model showed a training coefficient of determination (R2) of 0.98 and a root mean square error (RMSE) of 1.22 μg/m3. For the 10-fold cross-validation, the cross-validation R2 and RMSE of the model were 0.86 and 3.02 μg/m3, respectively. A subsite validation was used to validate the model at the grids overlapping with the AERONET sites, and the model performance was excellent at these sites with a validation R2 (RMSE) of 0.94 (1.78 μg/m3). Additionally, the model performance increased as increased AOD coverage. The top-ten important predictors for estimating ground PM2.5 concentrations were day of the year, temperature, AOD, relative humidity, 10-m-height zonal wind, 10-m-height meridional wind, boundary layer height, precipitation, surface pressure, and population density. MAIAC AOD showed high retrieval accuracy in Japan. The performance of the satellite-based model was excellent, which showed that PM2.5 estimates derived from the model were reliable and accurate. These estimates can be used to assess both the short-term and long-term effects of PM2.5 on health outcomes in epidemiological studies.