A cost-efficient photocatalytic oxidative denitrogenation and desulfurization system for fuels under visible light was developed on the basis of Na doped g-C3N4 nanosheets catalyst. The process adopted molecular O-2 as oxidant to substitute for the expensive H2O2, and it adapted to the removal of small molecules of pyridine and thiophene. Na doped g-C3N4 nanosheets were obtained via a simple mixed-calcination pathway using NaCl as Na source. The structural, photophysical and chemical properties of the photocatalysts were characterized and compared to those of the original g-C3N4. It was verified that Na was successfully doped in the g-C3N4 lattice in a uniform chemical state. Moderate amount of Na doped in g-C3N4 generated the highly dispersed and porous nanosheets, which further improved the surface energy and reduce the recombination rate of electron-hole pairs. Na doped g-C3N4 exhibited enhanced performance simultaneously in the photocatalytic oxidative denitrogenation and desulfurization. The optimal catalyst obtained considerable removal efficiency for pyridine and thiophene, depending on its improved structural and photochemical properties by Na doping. A proposed mechanism revealed that the holes acted as the major active species for the denitrogenation and desulfurization, while the superoxide radicals originating from the combination of electron and O-2 gave a promotion effect.