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Three-dimensional hierarchical nanoflowers self-assembled with the orthorhombic molybdenum oxide (α-MoO3) nanoflowers were synthesized by the modified hydrothermal method. The structure characterizations of the three-dimensional α-MoO3 nanoflowers were carried out by scanning electron microscope (SEM), Energy Disperse Spectroscopy (EDS), X-ray diffraction (XRD) and nitrogen adsorption-desorption measurement. Moreover, the three-dimensional α-MoO3 nanoflowers as photocatalyst exhibited enhanced photocatalytic activity towards photodegradation of Rhodamine B (RhB) under xenon (Xe) lamp irradiation. The results of SEM, EDS, XRD and nitrogen adsorption-desorption measurement showed the three-dimensional α-MoO3 nanoflowers have a better morphology, pore size (7.99 nm) and surface areas (50.788 m2 g−1) than hexagonal MoO3 (h-MoO3) nanosheets, photocatalytic activity studies confirmed that the three-dimensional α-MoO3 nanoflowers photocatalyst exhibits a high visible-light-driven activity for photodegradation of RhB solution of 91.57% within 160 min under Xe lamp irradiation. A mechanism was also proposed for the degradation of RhB by three-dimensional α-MoO3 nanoflowers.