A perfluorinated perylene diimide, N,N-diperfluorophenyl-3,4,9, 10-perylenetetracarboxylic diimide (DFPP), and its nonfluorinated analogue, N,N'-diphenyl-3,4,9, 10-perylenetetracarboxylic diimide (DPP), showed similar UV-vis absorption and fluorescence spectra when they existed as monomeric dyes in solutions, whereas in solid films they exhibited great differences. Absorption band splitting was observed for DPP film; however, for DFPP film, the fine structure of absorptions similar to that in solution still remained in addition to the absorption peaks becoming broader and shifting to longer wavelength regions. Furthermore, it was found that DFPP molecules aggregated to form a crystalline film when the temperature of the substrate was elevated to 200 degreesC. Through the simulation of the molecular conformation, the theoretical examinations of molecular interactions, the measurement of electron affinity, the observation of the film morphology by AFM and SEM, and the crystalline structure characterization by XRD, the unique aggregate structure of the crystalline DFPP thin film was suggested: DFPP molecules stacked with the perfluorinated phenyl groups straight over or below the perylene cores of the adjacent DFPP molecules.