A cluster magnetorheological (MR) electro-Fenton composite polishing technique was proposed in this work, which can realize high efficiency, ultra-smooth and damage-free of GaN wafer by the synergistic effect of electro-Fenton reaction and flexible mechanical removal of MR polishing. The key parameters of electro-Fenton were optimized through methyl orange degradation experiments based on experimental BBD method. The results showed that the decolorization rate had a strong dependence on H2O2 concentration, Fe-C concentration and pH value, where the decolorization rate had the maximum value when the H2O2 concentration of 5 wt%, Fe-C concentration of 3 wt% and pH value of 3. Compared with the Fenton reaction, the decolorization and REDOX potential of methyl orange solution were significantly improved in the electro-Fenton reaction. Furthermore, the process parameters of the cluster MR electro-Fenton composite polishing were optimized to obtain the best polishing result, which was realized under the conditions of 3 wt% diamond (grain size: 0.5 µm), a polishing gap of 0.9 mm and a polishing time of 60 min. The novel method achieved a material removal rate (MRR) of 10.79 μm/h, which was much higher than that of the conventional technique. In addition, an ultra-smooth and damage-free surface with a roughness of 1.29 nm Ra was obtained.