Graphene quantum dots (GQDs) have fascinating photoluminescence (PL) properties with promising applications in bioimaging, fluorescent sensing and the photoelectrics field. In this work, PL properties of GQDs obtained from different carbonaceous precursors including carbon fibers, graphite powder, graphene oxide (GO) and reduced graphene oxide (RGO) were regulated via a simple hydrothermal reduction. Upon hydrothermal treatment, the fluorescent peaks of the original GQDs were blue-shifted to 440 nm and their PL intensities were enhanced by about 2 times. Furthermore, the full widths at half maxima (FWHM) of the fluorescent peaks were narrowed. The improved PL properties of the GQDs were mainly attributed to the change of oxygenated groups on the GQDs surface, with most hydroxyl and epoxy groups of the GQDs removed, while carboxyl groups were largely intact. Different from chemical modification methods, the improvement of PL properties of GQDs by a hydrothermal method revealed the effect of different oxygenated groups on the GQDs surface on their PL properties, helping to clarify the PL mechanism of GQDs.