Oxygen diffusivity and surface exchange kinetics underpin the ionic, electronic, and catalytic functionalities of complex multivalent oxides. Towards understanding and controlling the kinetics of oxygen transport in emerging technologies, it is highly desirable to reveal the underlying lattice dynamics and ionic activities related to oxygen variation. In this study, the evolution of oxygen content is identified in real-time during the progress of a topotactic phase transition in La0.7Sr0.3MnO3-δ epitaxial thin films, both at the surface and throughout the bulk. Using polarized neutron reflectometry, a quantitative depth profile of the oxygen content gradient is achieved, which, alongside atomic-resolution scanning transmission electron microscopy, uniquely reveals the formation of a novel structural phase near the surface. Surface-sensitive x-ray spectroscopies further confirm a significant change of the electronic structure accompanying the transition. The anisotropic features of this novel phase enable a distinct oxygen diffusion pathway in contrast to conventional observation of oxygen motion at moderate temperatures. The results provide insights furthering the design of solid oxygen ion conductors within the framework of topotactic phase transitions.