Molecules of perylene tetracarboxylic diimide (PTCDI) form a unique class of n-type semiconductor, and have been widely used in various optoelectronics devices. Although some organized structures (e.g., particles, networks) have been fabricated from these molecules, the one-dimensional (1D) self-assembly (e.g., nanowire) of PTCDI remains challenging. One of the major challenges lies in the control and optimization of the effect of side-chain substitutions. In this study, such a side-chain effect was studied with two PTCDI derivatives modified with two distinct side-chains, dodecyl (linear) and nonyldecyl (branched). 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. Moreover, the distinct morphologies of self-assembly were obtained from both the solution-based processing and surface-supported solvent vapor annealing.