Graphitic carbon nitride (g-C3N4), an environment-friendly metal-free photocatalysts represent a promising alternative to conventional metal-based semiconductors. Although sp(2)-structured carbon-dot modified g-C3N4 has shown its effectiveness to enhance the photocatalytic efficiencies, a precise, comprehensive and molecular level understanding of this enhancement is demanded for advance progress, which is lacking due to the complexity of the samples in experiments. Here, our density functional theory (DFT) and time-dependent DFT calculations reveal that a precise graphene quantum dot (GQD) sensitization of g-C3N4 nanosheet significantly enhance excited-state charge separation, which is crucial for the photocatalytic activity. Nitrogen to carbon ratio is critical for the spatial separation of photogenerated electron-hole pair via GQD/g-C3N4 pi-pi stacking. Red-shift in the lowest excitation of GQD/g-C3N4 with size increment stretches the absorption to the visible wavelengths, facilitating the visible-light photocatalytic activity of g-C3N4. The mechanism revealed in this study supports the recent experimental reports on the competence of the environmental friendly, low cost and stable GQD sensitized g-C3N4 photocatalyst and provides guidance for optimal design to achieve higher efficiency.