Recently, various degradation mechanisms of lithium secondary battery cathode materials have been revealed. As a result, many studies on overcoming the limitation of cathode materials and realizing new electrochemical properties by controlling the degradation mechanism have been reported. Li-rich layered oxide is one of the most promising cathode materials due to its high reversible capacity. However, the utilization of Li-rich layered oxide has been restricted, because it undergoes a unique atomic structure change during the cycle, in turn resulting in unwanted electrochemical degradations. To understand an atomic structure deterioration mechanism and suggest a research direction of Li-rich layered oxide, we deeply evaluated the atomic structure of 0.4Li2MnO3_0.6LiNi1/3Co1/3Mn1/3O2 Li-rich layered oxide during electrochemical cycles, by using an atomic-resolution analysis tool. During a charge process, Li-rich materials undergo a cation migration of transition metal ions from transition metal slab to lithium slab due to the structural instability from lithium vacancies. As a result, the partial structural degradation leads to discharge voltage drop, which is the biggest drawback of Li-rich materials.