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.