We developed a new method to introduce N-vacancies of graphitic carbon nitride (GCN, typically in the Melon structure) at the inter-triazine sites and investigated how the visible-light photocatalytic H-2 evolution of GCN is affected by the N-vacancies at the intra- and inter-triazine sites of GCN. Theoretical and experimental results show that these N-vacancies of GCN create singly-occupied defect states within the band gap acing as a trap for photogenerated electrons and act as the reaction sites for H+ reduction. Compared with the intra-triazine N-vacancy, the inter-triazine N-vacancy exhibits stronger electron localization leading to a more efficient H-2 evolution. The photocatalytic reaction rate of GCN with inter-triazine N-vacancies is 9 times higher than that of "defect free" GCN, and 2.2 times higher normalized reaction rates than GCN with intra-triazine N-vacancies. The catalysis mechanism and the method to prepare melon with inter-triazine N-vacancies can be extended to explore new photocatalysts with high activities.