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 TiO2‐SrTiO3@TiO2 structure is developed inside an intercalated TiO2‐SrTiO3 core as “yolk” decorating densely packed flake TiO2 as shell, creating plentiful nano‐heterointerfaces with a continuous TiO2 and SrTiO3 “in‐house” interfaces, as well the interfaces between TiO2‐SrTiO3 yolk and TiO2 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 TiO2‐SrTiO3 composite electrolyte. Consequently, a single fuel cell based on the TiO2‐SrTiO3@TiO2 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.