To overcome the voltage decay upon cycling and increase the initial coulombic efficiency of the layered Li-rich Mn-based oxides, the double modification combining Na2S2O8 treatment with CaF2 coating has been first proposed in this study. The precondition Na2S2O8 treatment activates the Li2MnO3 phase gently and generates a stabilized three-dimensional spinel structure on the surface of particles, leading to a suppression of surface reaction and structure conversion during the subsequent electrochemical process. The mitigation of phase transformation for Na2S2O8-treated Li1.2Mn0.54Ni0.13Co0.13O2 alleviates the voltage decay and energy density degradation upon long-term charge-discharge cycling. In order to further restrain the capacity loss derived from the HF attack and manganese dissolution, 40 wt% Na2S2O8 treated-sample has been modified by an amorphous CaF2 layer with nano-scale thickness. The first-reported CaF2-coated/40 wt% Na2S2O8 treated-Li1.2Mn0.54Ni0.13Co0.13O2 presents excellent electrochemical properties with a high initial coulombic efficiency of 99.2%, a capacity retention rate of 89.2% after 200 cycles and a high-rate capability of 152.1 mAh g−1 at 3C. The double surface modification offers a smart design concept for Li-rich Mn-based oxides to meet the practical requirements for advanced lithium ion batteries in electric vehicles.