Aliovalent cation-doped perovskite-type oxides (ABO(3)) exhibit proton conductivity originating from the hydration of oxide ion vacancies, which is accompanied by structural deformation, i.e. chemical expansion. The chemical expansion may lead to failure in electrochemical devices, and thus it is necessary to understand the causes of this process at the atomic scale. In this study, the chemical expansion behaviors of Y-doped strontium cerate and zirconate were comparatively investigated. High-temperature X-ray diffraction (HT-XRD) and thermogravimetric analysis (TGA) revealed that the cerate exhibits larger chemical expansion. Density Functional Theory (DFT) calculations revealed that this tendency can be accounted for by the different atomic distribution of the Y dopant between the cerate and zirconate, which results in differences in the size of the oxide ion vacancies to be hydrated as well as different elastic character.