The chemical composition and structure of fine aerosol particles with diameters of less than 1 µm were analyzed in the spring of 2011 at Fukue Island, Japan, using an aerosol quadrupole mass spectrometer (Q-AMS, Aerodyne Research, Inc.) and a time-of-flight secondary ion mass spectrometer (TOF-SIMS). The Q-AMS results were similar to those of previous studies conducted at the same location, suggesting that the composition we observed is typical of this site. Based on the TOF-SIMS results, we classified the fine aerosol particles into three types: Type A, in which sulfate was covered with organic matter (OM); Type B, in which soil-containing particles with a diameter of 0.5 µm were associated with sulfate and OM; and Type C, in which black carbon (BC) and sulfate aggregates were associated with OM. During the observation period, the relative abundances of Type A, B, and C particles were 55%, 20%, and 25%, respectively. The structure, chemical composition, and the proportion of each type of particles provide information for a more representative particle model in radiative models. The relative abundance of Type C, i.e., BC-containing particles, is quite different to that in Tokyo, suggesting that Type C could be an indicator of transboundary air pollution, in this case from mainland China.