In this work, we apply materials informatics (MI) techniques for property prediction of nanoporous carbon-based electrocatalyst for oxygen reduction reaction (ORR), which is a key, but sluggish reaction in proton exchange membrane fuel cells and metal–air batteries. Nitrogen-doped graphene nanomesh (NGM) was identified as an appropriate ORR catalyst by the MI techniques, which is a useful support to producing designed nitrogen-coordinated single-atom catalysts via pyrolysis-free pathway. Herein, single-atom catalysts (FePc/NGM) with predictable structures were fabricated by anchoring iron phthalocyanine (FePc) on the MI-guided NGM. Compared with the randomly creating Fe-Nx moieties on a carbon matrix via pyrolysis, FePc were riveted onto NGM via axial interactions between Fe-N4 moieties in FePc and nitrogen in NGM graphene matrix. As a result, Fe-N5 with superior catalytic activity for ORR was created. The elaborately designed FePc/NGM possesses an outstanding electrocatalytic activity owing to its low-dimensional structure and the significant change in electronic and geometric structures arising from the rehybridization of Fe 3d orbitals from FePc with the nitrogen orbitals from NGM at the axial direction. This work demonstrates that fusion of experiments with material informatics is indispensable for the practice of the inorganic synthetic chemistry.