Atomic dispersed Fe-based catalysts (Fe-N-C) are a promising class of non-noble metal oxygen reduction reaction (ORR) materials. However, their practical application is severely limited by slow mass transfer and insufficient oxygen supply at device level, like the fuel cells. Herein, we report a rational design of a unique yolk-shell nanostructured catalyst (Fe-N-C_T) with triple-layer actives site distribution, exhibiting competitive ORR performance. Comprehensive characterization confirms its unique yolk-shell nanostructure, showing that the Fe-Nx moieties are atomically dispersed in the core, inner shell, and outer surface, significantly improving the active site density. Fe-N-C_T exhibits excellent ORR activity and stability in acidic media. Integration into an H₂-air fuel cell achieves a peak power density of 496 mW·cm⁻² and maintained stable operation with minimal voltage drop during 30,000 accelerated durability cycles. In-situ Raman spectroscopy and COMSOL simulations show that the unique yolk-shell structure acts as an oxygen reservoir, enriching O₂ molecules and reducing mass transfer polarization, thereby achieving excellent ORR performance at the device level.