The bandgap in graphene-based materials can be tuned from 0 eV to that of benzene by changing size and/or surface chemistry, making it a rising carbon-based fluorescent material. Here, the surface chemistry of small size graphene (graphene quantum dots, GQDs) is tuned programmably through modification or reduction and green luminescent GQDs are changed to blue luminescent GQDs. Several tools are employed to characterize the composition and morphology of resultants. More importantly, using this system, the luminescence mechanism (the competition between both the defect state emission and intrinsic state emission) is explored in detail. Experiments demonstrate that the chemical structure changes during modification or reduction suppresses non-radiative recombination of localized electron-hole pairs and/or enhances the integrity of surface π electron network. Therefore the intrinsic state emission plays a leading role, as opposed to defect state emission in GQDs. The results of time-resolved measurements are consistent with the suggested PL mechanism. Up-conversion PL of GQDs is successfully applied in near-IR excitation for bioimaging.