Vacancy-ordered perovskite oxides are attracting attention due to their diverse functions such as resistive switching, electrocatalytic activity, oxygen diffusivity, and ferroelectricity. It is important to clarify the chemical lattice strains arising from compositional changes and the associated vacancy order–disorder phase transitions at the atomic scale. Here, we elucidate the intermediate process of a topotactic phase transition in Ca-doped bismuth ferrite films consisting of alternating stacks of oxygen perovskite layers and a brownmillerite-type oxygen vacancy layer. We use Raman spectroscopy and transmission electron microscopy to closely examine the evolution of local strains exerted on the constituent sub-layers by electrochemical oxidation. A negative Raman chemical shift is observed during oxidation, which is linearly correlated with the local negative chemical expansivity of the oxygen layer. It seemingly contradicts with the general trend that oxides undergo lattice contraction upon oxidation. Oxygen vacancies initially confined in the vacancy layers can be understood to diffuse into the oxygen layers during melting of the ordered structure. The finding deepens our understanding of the electro-chemo-mechanical coupling of vacancy-ordered oxides.