With the development of photocatalytic hydrogen production technology, the effective transport of photogenerated carrier electrons is still one of the main factors affecting the performance of photocatalytic hydrogen evolution. In this work, graphdiyne was prepared by ball milling method. The CoMo-MOF with polyhedral structure was introduced into graphdiyne to construct S-scheme heterojunction to promote the efficient transfer of photogenerated carriers and enhanced hydrogen evolution activity. Graphdiyne is a new carbon material with adjustable band gap, which is synthesized from the hybrid of sp and sp2, and has excellent electrical conductivity. CoMo-MOF is a polyhedral structure that can provide more active sites and promote photocatalytic hydrogen evolution. The weak point of poor conductivity in CoMo-MOF has been successfully improved by combining CoMo-MOF with graphdiyne, and the migration rate of photogenerated carriers has been accelerated. The hydrogen evolution property of graphdiyne/CoMo-MOF is 300 μmol, which is 19.61 times that of graphdiyne and 9.03 times that of CoMo-MOF. Therefore, the construction of S-scheme heterojunction provides a transport channel for electron transfer and improves the efficiency of photogenerated carrier separation. This work provides a new train of thought of design to introduce MOFs materials into carbon materials for photocatalytic hydrogen evolution.