In this work, we report a simple, facile and effective method to simultaneously hydrogenate and exfoliate graphitic-C3N4 (g-C3N4) through high concentration sulfuric acid treatment. The hydrogenation mechanism of gC(3)N(4) is explained experimentally and it is further revealed in detail by molecular structure dynamics as well as the corresponding electronic structure evolutions. Five different atomic sites in unit cell of g-C3N4 are structurally available to be hydrogenated, and four of them are energetically favored to form hydrogenated structures. Different from the pristine g-C3N4 that is flat in basal plane, the energetically favored hydrogenation structure of g-C3N4 possesses the corrugated fluctuation plane. The hydrogenated g-C3N4 structures also present blueshifted UV vis absorption and photoluminesce (PL) peaks compared to that of pristine g-C3N4, and it is well explained by theoretical calculation results that the bandgap becomes larger due to hydrogenation. Finally, it is found that the photocatalytic performance of g-C3N4 is dramatically enhanced once the crystal structure is hydrogenated. The enhanced photocatalytic performance is mainly attributed to the hydrogenation caused spatial charge separation due to the redistribution of charge density in both valence band maximum and conduction band minimum. The revealing of spatial charge separation provides insight into the deep understanding of hydrogenation mechanism of g-C3N4, which is critically significant for designing light-efficient photocatalysis.