Among carbon allotropes, 2D graphdiyne (GDY) possesses the merits of good ductility, strong conductivity and an adjustable energy band structure. In this study, a GDY/ZnCo-ZIF S-scheme heterojunction photocatalyst has been successfully prepared by a low-temperature mixing method. Using eosin as a photosensitizer and triethanolamine as a solvent, the hydrogen production of the GDY/ZnCo-ZIF-0.9 composite reaches 171.79 μmol, which is 6.67 and 13.5 times that of the GDY and ZnCo-ZIF materials, respectively. The apparent quantum efficiency of the GDY/ZnCo-ZIF-0.9 composite at 470 nm is 2.8%. The improved photocatalytic efficiency may be attributed to the creation of an S-scheme heterojunction structure that enables efficient separation of space charges. In addition, the EY-sensitized GDY/ZnCo-ZIF catalyst endows the GDY with a special structure to provide an abundance of electrons for the ZnCo-ZIF material, thus facilitating the photocatalytic reduction reaction to produce hydrogen. A novel perspective is presented in this study regarding the construction of an S-scheme heterojunction based on graphdiyne for efficient photocatalytic hydrogen generation.