•Mn(MoO3)(SeO3)(H2O) has been hydrothermally synthesized at 160 °C with a high yield.•Mn(MoO3)(SeO3)(H2O) features a complicated 3D network.•Mn(MoO3)(SeO3)(H2O) is stable up to approximately 340 °C.•There exists antiferromagnetic interactions between Mn(II) centers in compound.•The compound exhibits good photocatalytic activity under visible light irradiation.A new phase in the MnII–SeIV–MoVI–O system, Mn(MoO3)(SeO3)(H2O) (1), has been hydrothermally synthesized with a high yield (82%), and characterized by IR, TG-DSC, magnetism measurement and single crystal X-ray diffraction. The structure of Mn(MoO3)(SeO3)(H2O) features a complicated 3D network composed of the 1D molybdenum(VI) oxide chains and the 1D manganese(II) selenite chains interconnected via Se–O–Mo and Mn–O–Mo bridges. It is stable up to approximately 340 °C, and losses water molecule at 340 °C, then release SeO2 at about 420 °C. The result of magnetic property measurements has indicated that there exist antiferromagnetic interactions between Mn(II) centers. Photocatalysis experimental result illustrates that the compound exhibits good photocatalytic performance for degradation of RhB under visible light irradiation.