Engineering of the defective structure and crystallinity of semiconductor photocatalysts to promote carrier dynamics has attracted considerable attention. This study presents the design of surface nitrogen defect modified crystalline carbon nitride spheres (QCN) with synergistically boosted surface and bulk carrier separation through a rapid thermal treatment coupled with a flux assisted strategy. Using supramolecular self-assembled polymer as the precursor, spherical crystalline CN heterojunctions are firstly prepared by a molten salt method to improve the separation of bulk carriers. Abundant nitrogen defects are then introduced onto the surface of crystalline CN through the following quick thermal treatment in air, which can generate a higher exciton density and drive rapid migration of surface carriers by acting as effective electron sinks. Furthermore, the defect level also improves the visible light utilization and provides more active centers for reactant adsorption and activation. As a result, QCN samples exhibit excellent performance in photocatalytic hydrogen evolution, with an optimal hydrogen production rate 4.3 times higher than that of pristine bulk CN under visible light irradiation. Moreover, the photocatalytic activities of QCN are dependent on the concentration of nitrogen defects, which can be flexibly adjusted via thermal treatment temperature. Such a two-step regulation strategy combining the distinctive advantages of surface defect structure and high crystallinity is beneficial for synergistic enhancement of photocatalytic performance, and provides new insights for sustainable energy production in the future.