Controllable nanostructures with tunable dimensions were obtained via self-assembly of CBZ-L-lysine-functionalized tetrachloroperylene bisimides (4ClPBI-Lys). Depending on the nature of substitute, solvent polarity, and sample concentration, 4ClPBI-Lys could form nanosphere, nanowire, nanobelt, and nanosheet, which were found to have different degree of molecular ordering. The effects of substitution position with respect to L-lysine on 4ClPBI were also explored in terms of assembly nanostructures. Hydrogen bonding was important to promote formation of long-range ordering. The nanostructures of different assemblies were characterized using SEM, TEM, XRD, UV-vis, and FTIR spectroscopy. For each obtained supramolecular assembly, we also found that the molecular packing motif ultimately determined the corresponding devices electronic properties.