WO3/Bi2WO6 heterojunctions with flower-like structure were prepared by a facile hydrothermal process without any surfactants or templates. In the heterojunctions, WO3 nanoparticles were incorporated into three-dimensional flower-like hierarchical Bi2WO6. The WO3/Bi2WO6 samples showed much higher photocatalytic activity than pure Bi2WO6 did for rhodamine B degradation under visible light irradiation. This could be ascribed to the formation of n-n type heterojunction, which resulted in the high transfer rate of the photo-generated electron-holes between WO3 and Bi2WO6 and confirmed by photoluminescence and photocurrent measurements.