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A water-gas shift reaction (WGS) is important and widely applied in the production of H2. Cu-modified perovskites are promising catalysts for WGS reactions in hydrogen generation. However, the structure-dependent stability and reaction pathways of such materials remain unclear. Herein, we report catalytically active Cu-modified SrTiO3 (nominally SrTi1-xCuxO3) prepared by a modified polymeric precursor method. Microstructural analysis revealed a partially segregated CuO phase in the as-prepared materials. Operando X-ray diffraction and absorption spectroscopy showed the reduction of CuO into a stable metallic phase under conditions of WGS reactions for all compositions. Among the characterized materials, the x = 0.20 composition showed the highest turnover frequency, lowest activation energy, and the highest WGS rate at 300 °C. According to density functional calculations, the formation of CuO is energetically less favorable compared with SrTiO3, explaining why the segregated CuO phase on the SrTiO3 surface is reduced to Cu during the catalytic reaction, while SrTiO3 remains. For x = 0.20, the size of the segregated CuO phase is optimum for facilitating the catalytic reaction. In contrast, a higher Cu content (x = 0.3) results in an aggregation of smaller CuO particles, resulting in fewer surface active sites and a net decrease in catalytic performance.