Cobalt-nitrogen/carbon (Co-N/C) was considered as the promising catalyst for oxygen reduction reaction (ORR). The combination of dense single-atom active site density and serviceable proton electronic conductivity is the key to improve the activity and stability of the catalyst in proton exchange membrane fuel cells. Herein, we achieved the in-situ growth of massive carbon nanotubes (CNTs) during the synthesis of Co-N/C catalysts by precisely regulating the ratio of reactants in the metal–organic framework precursors. Notably, the dense deformed Co-N4 sites were anchored on the in-situ grown CNTs, improving the triple-phase boundary and proton electronic conductivity of membrane electrode assemblies (MEA). Benefiting from the unique structure of dense Co-N4 sites anchored on CNTs, the target catalyst Co-N/C-1/4.4 exhibited high activity in both ORR (half-wave potential: 0.781 V, kinetic [email protected] V = 2.25 mA cm−2) and fuel cell (H2-Air: 0.49 W cm−2) tests. And the in-situ grown CNTs with high graphitization degree led to a significant improvement in the stability of the catalyst (10 mV decay of half-wave potential after 30,000 cycles). We believe this research may provide new understanding into the development of non-PGM electrocatalysts with high performance at the atomic scale.