We report on the mechanism for hydrogen-induced topotactic phase transitions in perovskite (PV) oxides using La0.7Sr0.3MnO3 as a prototypical example. Hydrogenation starts with lattice expansion confirmed by X-ray diffraction (XRD). The strain- and oxygen-vacancy-mediated electron-phonon coupling in turn produces electronic structure changes that manifest through the appearance of a metal insulator transition accompanied by a sharp increase in resistivity. The ordering of initially randomly distributed oxygen vacancies produces a PV to brownmillerite phase (La0.7Sr0.3MnO2.5) transition. This phase transformation proceeds by the intercalation of oxygen vacancy planes confirmed by in situ XRD and neutron reflectometry (NR) measurements. Despite the prevailing picture that hydrogenation occurs by reaction with lattice oxygen, NR results are not consistent with deuterium (hydrogen) presence in the La0.7Sr0.3MnO3 lattice at steady state. The film can reach a highly oxygen-deficient La0.7Sr0.3MnO2.1 metastable state that is reversible to the as-grown composition simply by annealing in air. Theoretical calculations confirm that hydrogenation-induced oxygen vacancy formation is energetically favorable in La0.7Sr0.3MnO3. The hydrogenation-driven changes of the oxygen sublattice periodicity and the electrical and magnetic properties similar to interface effects induced by oxygen-deficient cap layers persist despite hydrogen not being present in the lattice.