The tightness of π-π stacking in supramolecular organic semiconductors plays a crucial role in governing the spatial separation and migration dynamics of photogenerated charge carriers, ultimately determining their photocatalytic performance. To achieve close π-π stacking, the suitable design of molecular structure is essential. Therefore, two isomers of pyridine carboxylic acid-modified perylene monoimide (PMI) were designed and synthesized, namely PM5A and PM6A. In aqueous solution, these molecules self-assemble into aggregates, which exhibit distinct stacking properties and optical characteristics. Upon photoexcitation, the loose π-π stacking of PM5A favors the generation of charge-transfer excitons (CTEs) over charge-separation excitons (CSEs). In contrast, PM6A, stabilized by intermolecular hydrogen bonds and possessing close π-π stacking, undergoes efficient charge separation (CS) to produce CSEs within 4.5 picoseconds. When incorporated into metal-insulator-semiconductor (MIS) photosystems with polyvinylpyrrolidone (PVP)-capped Pt, the Pt/PVP/PM6A system demonstrates a hydrogen evolution rate (HER) of 8100 μmol g−1 h−1, nearly five times higher than that of the Pt/PVP/PM5A system. Additionally, the maximum apparent quantum efficiency (AQE) reaches approximately 2.1% under irradiation with light of a single wavelength of λ = 425 nm.