The poor selectivity and activity of the photocatalysts developed has hindered the photocatalytic production of hydrogen peroxide (H2O2). Therefore, modification techniques need to be pursued to improve the selectivity and activity of photocatalysts toward the two-electron oxygen reduction reaction. In this study, homogeneous self-modification by nitrogen vacancies is adopted as an efficient technique to narrow the band gap and induce the mid-gap states in the nanostructures of g-C3N4 synthesized by cyanuric acid–melamine supramolecular adducts. The presence of the vacancies in the structure and their respective effects on the optoelectronic features of the catalysts were thoroughly investigated by different characterizations. The optimized photocatalyst showed greatly improved H2O2 production of 200 μM under 1 h visible light irradiation, as compared with that of the bulk (35 μM) and the pristine nanostructured sample (85 μM), with acceptable reusability. This study also provides a new perspective on devising synergistic approaches to modify the performance of supramolecular-based carbon nitride photocatalysts.