As the next-generation high energy capacity cathode materials for Li-ion batteries, Ni-rich oxides face the problem of obtaining near-stoichiometric phases due to excessive Ni occupying Li sites. These extra-Ni-defects drastically affect the electrochemical performance. Despite of its importance, the fundamental correlation between such defects and the key electrochemical properties is still poorly understood. In this work, using density-functional-theory, we report a comprehensive study on the effects of non-stoichiometric phases on properties of Ni-rich layered oxides. For instance, extra-Ni-defects trigger charge disproportionation reaction within the system, alleviating the Jahn-Teller distortion of Ni3+ ions, which constitutes an important reason for their low formation energies. Kinetic studies of these defects reveal their immobile nature, creating a “pillar effect” that increases the structural stability. Ab initio molecular dynamics revealed Li depletion regions surrounding extra-Ni-defects, which are ultimate responsible for the arduous Li diffusion and re-intercalation, resulting in poor rate performance and initial capacity loss. Finally, the method with combination of high valence cation doping and ion-exchange synthesis is regarded as the most promising way to obtain stoichiometric oxides. Overall, this work not only deepens our understanding of non-stoichiometric Ni-rich layered oxides, but also enables further optimizations of high energy density cathode materials.