Herein, a series of heterogeneous Fenton catalysts, Cu doped MnO2 (CDM), with different Cu/Mn molar ratios were prepared via a hydrothermal reaction. Meanwhile, detailed characterizations were used to study the structures of CDM, and it is amazing that the morphology of CDM changed from nanowires to nanoflowers with an increasing amount of Cu doped. Apart from this, both the specific surface area and oxygen vacancy increased obviously with the increasing Cu/Mn molar ratio. Then, the degradation of different dyes was utilized to evaluate the catalytic activity of different CDM with H2O2 used as the oxidizing agent, and the 50%-CDM with the highest content of Cu doped displayed the best catalytic activity. Herein, the degradation efficiency (D%) of Congo red (CR) solution with low concentration (60 mg/L) reached 100% in 3 min, while the D% of CR solution with a high concentration (300 mg/L) reached 99.4% after 5 min with a higher dosage of H2O2. Additionally, the 50%-CDM also displayed excellent reusability, for which the D% values were still higher than 90% after the 14th cycles. Based on the structure characteristics and mechanism analysis, the excellent catalytic capacity of 50%-CDM was due to the combined influence of large specific surface area and abundant oxygen vacancy. Thus, a promising heterogeneous Fenton catalyst was developed in this study, which proved the treatment efficiency of actual dye wastewater.