Li-rich Co-free Mn-based oxides are known as prospective cathode in Li-ion batteries originating from high energy density, environmentally friendliness and economically efficiency. However, the anion-involving redox process of the cathodes inevitably deteriorate the lattice structure, ultimately resulting in capacity fading and poor kinetics, which is closely related to the aggregated distribution of LiMn6 superstructure units. Herein, the sophisticated interplay between electrochemical performance and local structure controlled by synthesis conditions has been unlocked. It explores that the phase composition and local cationic ordering of Li1.2Mn0.6Ni0.2O2 (LNM) at atomic scale can be adjusted by synthesis atmosphere. The material obtained under argon atmosphere exhibits robust layered structure with LiTMO2-like (TM: Ni, Mn) phase intergrew with Li2MnO3 phase at atomic scale, where the Ni ions partially occupied TM layer's sites of Li2MnO3, breaking the dispersion of LiMn6 superstructure unit. The obtained two phases coexistence structure at atomic level not only fully exploit the anionic redox activity but also stabilize the crystal structure during long-term cycling, which delivered an ultrahigh discharge capacity (303.4 mAh g−1 at 0.1 C) and outstanding cyclability (capacity retention of 88.1% after 500 cycles at 1 C). This work highlights the impact of synthesis conditions on the localized electronic structure and elucidates the structure-electrochemical performance relationship, providing novel insights in the design in cathode materials for advanced Li ion battery.