Tuning the microstructure of the catalyst surface is crucial for the loading of the co-catalyst, especially influencing the electron transfer and the size of the co-catalyst. However, influence of co-catalyst loading, related to the surface structure of the catalysts, is largely ignored. Here in, nitrogen vacancies were introduced to regulate the microstructure of carbon nitrogen and using this amorphous carbon nitride (ACN) with nitrogen vacancies as a substrate to provide atomic anchoring sites as well as electron sink to prevent Pt from further agglomeration. Experimental and theoretical results show that nitrogen vacancies were electron acceptors, which beneficial to reduce [PtCl6]2− by photo-generated electrons and consequently stabilize Pt ultra-small clusters located on the ACN. Furthermore, by combing structure and carrier behaviors, we infer that Pt ultra-small clusters stable location comes from the strong interaction between Pt and nitrogen vacancies. Pt ultra-small clusters improve electron transfer and boost photocatalytic hydrogen production. A delicate design modulates the catalyst microstructure to enhance interaction between the catalyst and the co-catalyst, resulting in a smaller co-catalyst size and provides a mean to create and optimize small size Pt-loaded and highly active photocatalysts.