Abstract A challenging task in solid oxide fuel cells (SOFCs) is seeking for an alternative electrolyte, enabling high ionic conduction at relatively low operating temperatures, i.e., 300–600 °C. Proton‐conducting candidates, in particular, hold a significant promise due to their low transport activation energy to deliver protons. Here, a unique hierarchical TiO 2 ‐SrTiO 3 @TiO 2 structure is developed inside an intercalated TiO 2 ‐SrTiO 3 core as “yolk” decorating densely packed flake TiO 2 as shell, creating plentiful nano‐heterointerfaces with a continuous TiO 2 and SrTiO 3 “in‐house” interfaces, as well the interfaces between TiO 2 ‐SrTiO 3 yolk and TiO 2 shell. It exhibits a reduced activation energy, down to 0.225 eV, and an unexpectedly high proton conductivity at low temperature, e.g., 0.084 S cm −1 at 550 °C, confirmed by experimentally H/D isotope method and proton‐filtrating membrane measurement. Raman mapping technique identifies the presence of hydrogenated HO─Sr bonds, providing further evidence for proton conduction. And its interfacial conduction is comparatively analyzed with a directly‐mixing TiO 2 ‐SrTiO 3 composite electrolyte. Consequently, a single fuel cell based on the TiO 2 ‐SrTiO 3 @TiO 2 heterogeneous electrolyte delivers a good peak power density of 799.7 mW cm −2 at 550 °C. These findings highlight a dexterous nano‐heterointerface design strategy of highly proton‐conductive electrolytes at reduced operating temperatures for SOFC technology.