Effect of side-chain substitutions on the morphology of self-assembly of perylene diimide molecules has been studied with two derivatives modified with distinctly different side-chains, N, N'-di( dodecyl)-perylene-3,4,9,10-tetracarboxylic diimide ( DD-PTCDI) and N, N'-di( nonyldecyl)-perylene-3,4,9,10-tetracarboxylic diimide ( ND-PTCDI). Due to the different side-chain interference, the self-assembly of the two molecules results in totally different morphologies in aggregate: one-dimensional ( 1D) nanobelt vs zero-dimensional ( 0D) nanoparticle. The size, shape, and topography of the self-assemblies were extensively characterized by a variety of microscopies including SEM, TEM, AFM, and fluorescence microscopy. The distinct morphologies of self-assembly have been obtained from both the solution-based processing and surface-supported solvent-vapor annealing. The nanobelts of DD-PTCDI fabricated in solution can feasibly be transferred to both polar ( e. g., glass) and nonpolar ( e. g., carbon) surfaces, implying the high stability of the molecular assembly ( due to the strong pi-pi stacking). The side-chain-dependent molecular interaction was comparatively investigated using various spectrometries including UV-vis absorption, fluorescence, X-ray diffraction, and differential scanning calorimetry. Compared to the emission of ND-PTCDI aggregate, the emission of DD-PTCDI aggregate was significantly red-shifted ( ca. 30 nm) and the emission quantum yield decreased about three times, primarily due to the more favorable molecular stacking for DD-PTCID. Moreover, the aggregate of DD-PTCDI shows a pronounced absorption band at the longer wavelength, whereas the absorption of ND-PTCDI aggregate is not significant in the same wavelength region. These optical spectral observations are reminiscent of the previous theoretical investigation on the side-chain-modulated electronic properties of PTCDI assembly.