In this work, we have synthesized Cu-doped MnO@diatomite successfully though a one-step hydrothermal approach. Meanwhile, application for degradation of methylene blue in Fenton-like system was investigated. The compounds were characterized by X-ray diffraction (XRD), X-ray photoelectron spectroscope (XPS), Inductively Coupled Plasma analysis (ICP) and UV-vis spectroscopy measurements, beam scanning electron microscope (FIB/SEM), energy dispersive X-ray spectrometer (EDS). The observations revealed that copper was indeed intercalated into layered structure of MnO and Density functional theory (DFT) calculations predicted that Cu intercalated MnO@diatomite brought about the narrowing of band gap and the enhancing of charge mobility during catalysis. Electron Density Difference of CuMnD demonstrated excellent oxidation ability to dissociate HO and generate hydroxyl radical (OH) to degrade the MB. Moreover, the proper copper doping of sample is more easily to form oxygen defect, which generate more surface hydroxyl groups as reaction sites for surface adsorption. In addition, the degradation efficiency of CuMnD was tremendously influenced by the initial pH, HO dosage and copper content of catalyst. Ultimately, 0.02-25-CuMnD along with molar ration of Cu/Mn with 0.4402 showed the best degradation efficiency which was about 96.2% within 4 h with 16.5 mM of HO and pH 2.06.