In this study, the catalytic potential of two representative covalent organic frameworks (COFs), COF-366 and Pc-PBBA COF, was investigated in the oxygen reduction reaction (ORR). Transition metal atoms (Fe or Co) were incorporated into the center of porphyrin or phthalocyanine rings to form Fe(Co)-N-C single-atom catalysts, which can catalyze the ORR with overpotentials between 0.49 V and 0.69 V. In order to improve the catalytic activity, we introduced graphene or C3N4 layers to build heterojunctions with the COFs. Charge density difference and Bader charge analysis demonstrated that the introduction of a graphene (or C3N4) layer increases the population of electrons on the Fe and Co ions, which facilitates the flow of electrons to the intermediates and promotes the ORR catalytic reaction. For COFs@graphene heterojunctions, the overpotential decreases by 10.9-20.3% for Fe-based active sites and 30.3-36.4% for Co-based active sites. For COFs@C3N4 heterojunctions, the overpotential decreases by 7.3-39.1% for Fe-based active sites and 15.116.3% for Co-based active sites. The analysis of the volcano plot reveals that the COF-366_Co@graphene heterojunction is positioned at the apex of the volcano plot with an overpotential of 0.31 V.