An unconventional method based on hot filament chemical vapor deposition system is used to fabricate MoO3−x/graphene nanoflake hybrid structures via surface growth. MoO3 precursor is firstly reduced to MoO3−x nanoparticles mediated by N2 molecules excited by electrons emission from hot tungsten filaments. Graphene nanoflakes are then grown on the MoO3−x nanoparticles in a high-flow-rate CH4 environment through the surface conversion of hydrocarbon radicals to benzene. The results indicate that the MoO3−x nanoparticles are mainly composed of Mo4O11 and MoO2 phases and they are covered by the graphene nanoflakes formed via surface growth. This new hybrid structure emits the ultraviolet, blue, green, red and infrared light and the photoluminescence of MoO3−x nanoparticles is quenched by the graphene nanoflakes. The generation of prevailing photoluminescence bands is interpreted by the three mechanisms including the near band edge emission, the transition between two bands and the inter-valence charge transfer transition, which indicates that the intermediate band formed within the bandgap by electrons from oxygen vacancies may cause the emission. The observed photoluminescence quenching of MoO3−x nanoparticles originates from the transfer of electrons from MoO3−x nanoparticles to graphene nanoflakes under electric field formed in the MoO3−x/graphene nanoflake interface. These results not only provide further insights into the rich surface properties of graphene/molybdenum oxide hybrid structures but also contribute to the design and synthesis of new materials and the development of next-generation graphene-based optoelectronic and photovoltaic devices.