Azobenzene (Azo) units were successfully introduced into perylene bisimide (PBI) structures in order to realize the photocontrolling of the morphology of the supramolecular assembly of PBI by a photoisomerization process. A total of three Azo-functionalized perylene bisimide derivatives (, , and ) with different alkyl chain lengths were designed and synthesized by imidization of 3,4,9,10-perylene tetracarboxylic dianhydride with the corresponding amines. The structures of these compounds were characterized by proton nuclear magnetic resonance (H NMR) and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS). The photoisomerization behaviors of Azo units in PBIs were investigated using ultraviolet-visible (UV-VIS) absorption spectroscopy, which were obviously effected by solvents and the alkyl chain length. Furthermore, the photoisomerization of Azo units has the obviously regulatory effect on the morphology of supramolecular assembly of PBIs, especially for the medium-length alkyl chain-linked Azo-functionalized PBI derivative (). This research realized the photocontrolling of the morphology of the supramolecular assembly of PBI derivatives by photoisomerization of Azo units.