Understanding Li+ ion diffusion pathways in Li-rich layered transition metal (TM) oxides is crucial for understanding the sluggish kinetics in anionic O2- redox. Although Li diffusion within the alkali layers undergoes a low-barrier octahedral-tetrahedral-octahedral pathway, it is less clear how Li diffuses in and out of the TM layers, particularly given the complex structural rearrangements that take place during the oxidation of O2-. Here, we develop simultaneous electron ptychography and annular dark field imaging methods to unlock the Li migration pathways in Li1.2Ni0.13Mn0.54Co0.13O2 associated with structural changes in the charge-discharge cycle. At the end of TM oxidation and before the high-voltage O oxidation plateau, we show that the Li migrating out of the TM layers occupies the alkali-layer tetrahedral sites on opposite sides of the TM layers, forming Li-Li dumbbell configurations, consistent with the density functional theory calculations. Also occurring are the TM migration and phase transition from O3 to O1 stacking, leading to unstable tetrahedral Li and the absence of Li contrast in imaging. Upon further Li deintercalation to 4.8 V, most of the tetrahedral Li are removed. After discharging to 2 V, we did not identify the reformation of tetrahedral Li but observed permanently migrated TMs at the alkali-layer sites, disfavoring the Li occupying the tetrahedral sites for diffusion. Our findings suggest a landscape of Li diffusion pathways in Li-rich layered oxides and strategies for minimizing the disruption of Li diffusion.