Graphitic carbon nitride (g-C3N4) based nanohybrids have drawn considerable attentions due to superior performances. However, the photoactivity of bulk g-C3N4 is limited due to the recombination of its photogenerated electron-hole pairs. Graphitic carbon nitride quantum dots (g-CNQDs), as a newly developed semiconductor, are easily prepared and possess good stability, water-solubility and electronic properties. In this work, we explored the fabrication of nanohybrids by in situ coupling of g-CNQDs and Bi2MoO6 nanoparticles (NPs). The as-prepared nanohybrids displayed nearly 3-fold and 6-fold enhanced photocurrent intensity than pure g-CNQDs and Bi2MoO6 NPs. This improvement was attributed to the accelerated charge transfer from the conduction band of g-CNQDs to that of Bi2MoO6. Based on the excellent photoelectrochemical (PEC) performances, the nanohybrids were successfully applied in the construction of Cu2+ PEC sensor. Under optimal conditions, the resulting sensor showed good performances with a wide linear range from 3nM to 40μM and a good selectivity, which indicated that g-CNQDs/Bi2MoO6 nanohybrids could serve as a promising photoactive material for PEC sensing.