N-doped graphene quantum dots (GQDs) are attracting great interest as promising Pt-free oxygen reduction reaction (ORR) catalysts. In this work, the mechanism of ORR on N-doped GQDs with three different sizes has been investigated based on density functional theory. Our results show that the size of the N-doped GQDs affects the ORR. The adsorption strength of ORR intermediates, the reaction free energy of the rate-determining step, and the overpotential increase with the increase of the size of N-doped GQDs. The N-doped GQDs with the smallest size possess the smallest overpotential, indicating the highest ORR catalytic activity. Our results will help to understand the size effect of N-doped GQDs on the catalytic activity of ORR.