The NASA/AERONET field campaign DRAGON/J-ALPS (Distributed Regional Aerosol Gridded Observation Networks/Joint work to the AerosoL Properties and Process Simulations) was conducted from March 2020 to May 2021 in Nagano, Japan. Twelve sun photometers were installed around Nagano prefecture. The effects of topography on aerosols were studied using observations and simulations. In this study, a regional chemical transport model (SCALE-Chem) was employed. Three numerical experiments were conducted: E1 (control experiment), E2 (E1 without topography), and E3 (E1 with removal of all anthropogenic emissions over Nagano prefecture). In E2, the terrain effect was not considered; the difference between E1 and E2 indicated the influence of mountains. The differences between E1 and E3 evaluate the local emission effect. In some cases, the mountainous terrain seemed to have suppressed aerosol inflow (i.e., reduced aerosol concentration), while in other cases, the mountains contributed to aerosol retention on days when aerosols tended to accumulate in mountain basins due to local emissions. Thus, while mountains prevent the inflow of aerosols from outside, they also contribute to increased aerosol concentration in the basin. Naturally, more significant effects are produced by meteorological conditions and the presence or absence of transboundary pollution from the outside. From observations and model simulations, we found that the aerosol concentration was not high around the J-ALPS site because of the mountain effect that prevents advection from the outside, even when transboundary pollution was observed in Japan in March 2020.