Polymer electrolyte membrane fuel cells (PEMFCs) suffer from severe performance degradation when operating under harsh conditions such as fuel starvation, shut-down/start-up, and open circuit voltage. A fundamental solution to these technical issues requires an integrated approach rather than condition-specific solutions. In this study, an anode catalyst based on Pt nanoparticles encapsulated in a multifunctional carbon layer (MCL), acting as a molecular sieve layer and protective layer is designed. The MCL enabled selective hydrogen oxidation reaction on the surface of the Pt nanoparticles while preventing their dissolution and agglomeration. Thus, the structural deterioration of a membrane electrode assembly can be effectively suppressed under various harsh operating conditions. The results demonstrated that redesigning the anode catalyst structure can serve as a promising strategy to maximize the service life of the current PEMFC system.