In photocatalytic degradation of pollutants, hydrogen-related defects on the catalyst surface inhibit the generation of highly reactive superoxide radicals (·O2−). Therefore, strategies to mitigate such defects are crucial for enhancing photocatalytic efficiency. To address this challenge, ZnWO4/hydrothermal red phosphorus (ZnWO4/HRP) S-scheme heterojunction photocatalysts were successfully prepared via a simple hydrothermal method, constructing a compact interfacial structure where rod-shaped ZnWO4 uniformly attaches to the HRP surface. Photocatalytic performance tests revealed that the composites exhibited excellent catalytic activity for rhodamine B (RhB) degradation, with a rate constant of 0.21 min−1 within 15 min-3.5 and 21 times higher than those of individual HRP and ZnWO4, respectively. Moreover, due to the robust chemical structure and strong interfacial bonding between ZnWO4 and HRP, the composite maintains high photocatalytic stability across multiple catalytic cycles. Mechanistic analysis demonstrates that the S-scheme heterojunction effectively suppresses the formation of hydrogen-related defects on the ZnWO4 surface, significantly reducing surface defect state density. This inhibition enhances photogenerated carrier separation, accelerates charge transfer, and facilitates the efficient generation of ·O2−. By adopting a heterojunction strategy to address hydrogen-related defects, the catalyst’s visible-light absorption capacity, photoelectric conversion efficiency, and radical generation efficiency was enhanced, while carrier recombination was suppressed. These findings provide new insights for designing high-efficiency heterojunction photocatalysts and highlight their promising potential in photocatalytic removal of organic pollutants.