The energy materials performance is intrinsically determined by structures from the average lattice structure to the atom arrangement, valence, and distribution of the containing transition metal (TM) elements. Understanding the mechanism of the structure transition and atom rearrangement via synthesis or processing is key to expediting the exploration of excellent energy materials. In this work, in situ neutron scattering is employed to reveal the real-time structure evolution, including the TM-O bonds, lattice, TM valence and the migration of the high-voltage spinel cathode LiNi0.5Mn1.5O4. The transition-metal-mediated spinel destabilization under the annealing at the oxygen-deficient atmosphere is pinpointed. The formation of Mn3+ is correlated to the TM migration activation, TM disordered rearrangement in the spinel, and the transition to a layered-rocksalt phase. The further TM interdiffusion and Mn2+ reduction are also revealed with multi-stage thermodynamics and kinetics. The mechanisms of phase transition and atom migrations as functions of temperature, time and atmosphere present important guidance on the synthesis in various-valence element containing oxides.