The inter-comparison of regional air quality models is an effective way to understand uncertainty in ambient pollutant concentrations simulated using various model configurations, as well as to find ways to improve model performance. Based on the outcomes and experiences of Japanese projects thus far, a new model inter-comparison project called Japan’s study for reference air quality modeling (J-STREAM) has begun. The objective of J-STREAM is to establish reference air quality modeling for source apportionment and effective strategy making to suppress secondary air pollutants including PM2.5 and photochemical ozone in Japan through model inter-comparison. The first phase focuses on understanding the ranges and limitations in ambient PM2.5 and ozone concentrations simulated by participants using common input datasets. The second phase focuses on issues revealed in previous studies in simulating secondary inorganic aerosols, as well as on the three-dimensional characteristics of photochemical ozone as a new target. The third phase focuses on comparing source apportionments and sensitivities under heavy air pollution episodes simulated by participating models. Detailed understanding of model performance, uncertainty, and possible improvements to urban-scale air pollution involving secondary pollutants, as well as detailed sector-wise source apportionments over megacities in Japan are expected.