The utilization of perovskite oxide as a catalyst for aqueous reactions is promising but challenging in stability. Here, we propose an in situ growth strategy that constructs an ultrathin protective skin on the Sr0.9Fe0.81Ta0.09Ni0.1O3-δ perovskite surface and thus effectively solves the stability issue. Using a spherical aberration-corrected transmission electron microscope, we observe the coexistence of an angstrom-scale (~7 Å) Fe2O3 protective skin and FeNi alloy nanoparticles. A number of alloy nanoparticles grow along with the skin and uniformly take root on the skin surface. Such a hierarchical structure can reconstruct the surface electronic structure and suppress the ion leaching of perovskite oxide in water. Benefiting from this unique structure, the catalyst has experienced a substantial increase (800 h, more than three orders of magnitude) in its stable operation time in water (for example, in a hydrogen evolution reaction). These results provide valuable insight into solid-solid phase transitions and have substantial implications for using structural defects at surfaces to modulate mass transport and transformation kinetics. Our strategy is sufficiently simple and can be used to subtly manipulate the catalyst structures to improve the performance of perovskite-based catalysts and potentially other oxide catalysts for a wide range of reactions.