Spatially separated HOMO-LUMO sites in the highly crystalline g-C3N4 can vastly facilitate the rapid transfer and separation of photogenerated charges to greatly improve its photocatalytic performance, which remains a great challenge to be achieved. In this study, the highly intra- and inter-plane crystalline g-C3N4 (c-CN) with the spatially separated HOMO-LUMO sites is explicitly produced through a moderate Na-modulated strategy to efficiently promote the directional transfer and separation of photoinduced charges. As a result, the optimized c-CN1.0 photocatalyst exhibits exceptional H2-evolution performance (313.5 μmol h−1, AQE = 13.38 %), which is ca. 14.3 times of the bulk g-C3N4. The excellent hydrogen-generation efficiency of c-CN photocatalyst is mainly ascribed to the synergism of high intra- and inter-layer crystallization of g-C3N4 and spatially separated HOMO-LUMO sites, which can vastly boost the directional transfer and effective separation of photoexcited electrons and holes. This research may open novel avenues to construct other photocatalysts with high efficiency.