Various Bi2MoO6 (BM)-based heterojunctions have been constructed to enhance the photocatalytic performance, but hydroxide/BM heterojunctions were rarely reported. To illustrate function of hydroxides in the heterojunctions for charge separation and photoactivity enhancement, In(OH)3/BM heterojunctions were simply prepared for the first time via in situ growth of In(OH)3 nanosheets on surfaces of BM hierarchical microspheres in a chemical precipitation process at the room temperature. Construction of the heterojunction benefits from formation of In-O-Bi/Mo bonds at the interface between BM and In(OH)3. Photoluminescence spectroscopy, time-resolved fluorescence spectroscopy, and photoelectrochemical tests demonstrate that the In(OH)3/BM heterojunction exhibits considerably accelerated separation of photoinduced charge carriers which results in increased generation rates of reactive oxygen species and enhanced photocatalytic degradation efficiencies for Rhodamine B, salicylic acid, and resorcinol, in comparison with pure BM. The heterojunction shows high chemical stability and satisfactory recyclability. This work provides a new BM-based heterojunction and, more importantly, deep insight into function of hydroxides in the heterojunction, which can direct preparation of other hydroxide-containing heterojunctions.