A scalable and controllable nanoscale perforation method for graphene is developed on the basis of the two-step thermal activation of a graphene aerogel. Different resistance to the thermal oxidation between graphitic and defective domains in the weakly reduced graphene oxide is exploited for the self-limiting nanoscale perforation in the graphene basal plane via selective thermal degradation of the defective domains. The resultant nanoporous graphene with a narrow pore-size distribution addresses the long-standing challenge for the high-level doping of graphene with lattice-mismatched large-size heteroatoms (S and P). Noticeably, this novel heteroatom doping strategy is demonstrated to be highly effective for oxygen reduction reaction (ORR) catalysis. Not only the higher level of heteroatom doping but also favorable spin and charge redistribution around the pore edges leads to a strong ORR activity as supported by density functional theory calculations.