Herein, self-assembly of hierarchical multihole g-C3N4 hexagon with excellent specific surface area (129 m2/g) and nitrogen vacancies were accomplished via a one-step polymerization of hydrothermal-treated dicyandiamide and ethylene-diamine-tetra-acetic acid (EDTA). The special chelate structure of EDTA efficiently enlarged a broad visible light response range, and the concentrations of EDTA promoted the self-assembly formation of different surface morphology. The photocatalytic H2 production rate under visible light for the optimal g-C3N4 hexagon (CN-20E) reaches 5839 μmol·g−1·h−1 and its apparent quantum efficiency reaches up to 7.3% at 420 nm, which has a 102 times higher for H2 production rate than that of bulk g-C3N4 (57 μmol·g−1·h−1). Special structure of the multihole hexagon endows them with remarkably visible light absorption, fast separation of photo-induced charge carriers, large surface areas as well as the exposure of potential photocatalytic active sites, thereby dramatically improved the H2 production property. Moreover, the forming process for the specific structure and the reaction mechanism of the enhanced photocatalytic activity were proposed according to the experimental results and theoretical calculations. This work exhibits a new avenue to rehandle graphitic carbon nitride precursor to build a grafted structure for developing highly efficient g-C3N4 in the practical photocatalytic application.