Herein, the preparation of Co3O4 QDs-Ag2MoO4 (AMO) heterojunction was reported by a facile hydrothermal method and characterized by physicochemical methods such as Fourier transformed infrared (FT-IR), X-ray diffraction (XRD), field emission scanning electron microscopy (FE-SEM), energy-dispersive X-ray spectroscopy (EDS), transmission electron microscopy (TEM), differential reflectance spectroscopy (DRS), photoluminescence spectroscopy (PL), and UV–Vis. The SEM images show that AMO particles and Co3O4 QDs-AMO have a morphology of 3D-hexagons and nanosheets accumulated on the surface of 3D-hexagons with an average of 36 and 28 nm in size, respectively. The Co3O4 QDs-AMO photocatalyst was used toward the conversion of methylene blue with a removal percentage of 91%, which is 15 times more than pure AMO. The higher photoactivity of Co3O4 QDs-AMO heterojunction should be assigned to its lower charge recombination rate compared with pure AMO nanoparticles. This heterojunction photocatalyst was removed from the mixture reaction and reused five times without a considerable decline in activity. Furthermore, a postulated mechanism by the hydroxyl radical (°OH) path was proposed.