Abstract One of the primary challenges in relation to phosphoric acid fuel cells is catalyst poisoning by phosphate anions that occurs at the interface between metal nanoparticles and the electrolyte. The strong adsorption of phosphate anions on the catalyst surface limits the active sites for the oxygen reduction reaction (ORR), significantly deteriorating fuel cell performance. Here, antipoisoning catalysts consisting of Pt‐based nanoparticles encapsulated in an ultrathin carbon shell that can be used as a molecular sieve layer are rationally designed. The pore structure of the carbon shells is systematically regulated at the atomic level by high‐temperature gas treatment, allowing O 2 molecules to selectively react on the active sites of the metal nanoparticles through the molecular sieves. Besides, the carbon shell, as a protective layer, effectively prevents metal dissolution from the catalyst during a long‐term operation. Consequently, the defect‐controlled carbon shell leads to outstanding ORR activity and durability of the hybrid catalyst even in phosphoric acid electrolytes.