Shape-controlled alloy nanoparticle catalysts have been shown to exhibit improved performance in the oxygen reduction reaction (ORR) in liquid half-cells. However, translating the success to catalyst layers in fuel cells faces challenges due to the more demanding operation conditions in membrane electrode assembly (MEA). Balancing durability and activity is crucial. Here, we developed a strategy that limits the atomic diffusion within surface layers, fostering the phase transition and shape retention during thermal treatment. This enables selective transformation of platinum-iron nanowire surfaces into intermetallic structures via atomic ordering at a low temperature. The catalysts exhibit enhanced MEA stability with 50% less Fe loss while maintaining high catalytic activity comparable to that in half-cells. Density functional calculations suggest that the ordered intermetallic surface stabilizes morphology against rapid corrosion and improves the ORR activity. The surface engineering through atomic ordering presents potential for practical application in fuel cells with shape-controlled Pt-based alloy catalysts.