Seasonal intensive sampling was undertaken for two weeks during each of four seasons from May 2015 to February 2017 at Niigata-Maki station in Niigata, eastern Japan. Daily mean concentrations of PM2.5 ranged from 4.2 µg m–3 to 33.4 µg m–3 during the observation period, which were lower than Japanese Environmental Quality Standard for PM2.5 (35 µg m–3). The higher concentrations of SO42−, NH4+ and OC were observed in spring and summer, which may result from photochemical activity and secondary OC production. The major chemical components of PM2.5 at Niigata-Maki site were SO42−, NO3−, NH4+, OCM, EC and crustal elements. Compared with data at other urban sites, a lower concentration of EC and NO3− and higher OC/EC ratio were observed at Niigata-Maki site, which may result from no significant stationary source and low vehicular traffic in the rural site. PM2.5 source apportionment was characterized by positive matrix factorization (PMF) analysis, and the results inferred four major sources: sea salt (10.2%), biomass combustion (18.9%), soil dust (13.2%) and secondary aerosol (44.4%). The potential source contribution function (PSCF) analysis suggested that the major sources of secondary aerosol and sea salts were domestic in southwest Japan and the Sea of Japan, whereas the sources of biomass combustion and soil dust in specific seasons were long range transportation from the Northeast Asian continent (NEA). Comparing with previous studies in western Japan, this study showed a large domestic contribution of southwest Japan for secondary aerosol, while a larger contribution of the NEA was observed in the previous studies. Significant contribution of biomass combustion from northeast China in autumn, and local area in Niigata and southwest Japan in the other seasons was uniquely observed in this study.