A novel Co3O4 quantum dots (CQDs)/2D graphdiyne (GDY) Z‐scheme heterojunction is fabricated by cross‐coupling reaction and electrostatic self‐assembly methods. GDY with the features of 2D porous structures has not only conducted the adsorption of dye molecules but also CQDs is facile to be anchored on the surface. Additionally, the construction of Z‐scheme heterojunction is conductive to conquer the shortcomings of easy agglomeration and poor dispersion for CQDs. The maximum photocatalytic hydrogen generation rate of 1500.85 µmol h−1 g−1 is gained for 30% GDY/CQDs and display an apparent quantum efficiency of 1.37% at 475 nm, which is roughly 11‐fold and 2.8‐fold higher than the pristine GDY and CQDs, respectively. The superior photocatalytic H2 production performance would be put down to the intense synergy of Z‐scheme heterostructure and the size effect of CQDs. They dramatically enhance the separation and transport of photogenerated charge carriers. Besides, the Z‐scheme charge transfer mechanism is further verified through the results of photoluminescence. This work offers new insight into the design of GDY‐based Z‐scheme heterojunction for photocatalysis.