In situ growth of zinc oxide (ZnO) nanoparticles (NPs) into self-assembled nanoclusters onto the surface of reduced graphene oxide (RGO) were obtained via a simple soft chemical approach at relatively low temperature (95 °C). A structural transformation of ZnO was observed from NPs to nanoclusters with the variation in concentrations of RGO contents under similar conditions which was clearly seen by TEM micrographs. It was observed that ZnO NPs come closer during nucleation and convert into nanoclusters of size 200–300 nm at the threshold RGO concentration. Furthermore, the effect of structural transformation and role of RGO concentration were evaluated against the degradation of Methylene Blue (MB) under UV as well as without any light source. The results demonstrate that RGO controls the loading and the morphology of ZnO, which improves the degradation performance of nanohybrids without any light source. Furthermore, ZnO-RGO-100 nanohybrid with highest RGO concentration shows excellent degradation behaviour without light irradiation as compared to their individual constituents.