The development of fuel cells as clean-energy technologies is largely limited by the prohibitive cost of the noble-metal catalysts needed for catalyzing the oxygen reduction reaction (ORR) in fuel cells. A fundamental understanding of catalyst design principle that links material structures to the catalytic activity can accelerate the search for highly active and abundant nonmetal catalysts to replace platinum. Here, we present a first-principles study of ORR on nitrogen-doped graphene in acidic environment. We demonstrate that the ORR activity primarily correlates to charge and spin densities of the graphene. The nitrogen doping and defects introduce high positive spin and/or charge densities that facilitate the ORR on graphene surface. The identified active sites are closely related to doping cluster size and dopant-defect interactions. Generally speaking, a large doping cluster size (number of N atoms >2) reduces the number of catalytic active sites per N atom. In combination with N clustering, Stone-Wales defects can strongly promote ORB.. For four-electron transfer, the effective reversible potential ranges from 1.04 to 1.15 V/SHE, depending on the defects and cluster size. The catalytic properties of graphene could be optimized by introducing small N clusters in combination with material defects.