With the development of the single-atom catalysts in electrocatalysis, the existence of metal nanoclusters in metal-N-C based materials have been proved. However, the effect of metal nanoclusters on electrocatalysis is hard to be confirmed. Herein, a novel framework of NCNTs with Fe nanoclusters and Fe-N-C sites (Fe3C-NCNTs 90min/CC) have been synthesized as the platform confirmed by Cs-corrected TEM and HADDF-STEM. Compared the samples immersed in HCl to remove Fe nanoclusters (HCl-Fe3C-NCNTs 90min/CC), the composite exhibits strong polarization and electron modulation effect onside the surface of NCNTs confirmed by holography. The electrocatalytic performance of Fe3C-NCNTs 90min/CC reduced significantly after the acid-treatment with a half-wave potential of 0.88 to 0.78V for ORR and an overpotential of 380mV to 510mV at 10mA cm− 2 for OER in alkaline solution. Furthermore, such a bifunctional catalyst endows the homemade ZAB with high power density and long-term stability, outperforming commercial Pt/C-RuO2 catalysts. The density functional theory (DFT) calculation indicates that the multiatom Fe-N-C sites significantly accelerate the desorption of OH* intermediates and thus promote the ORR process. This work paves a facile route to design the cluster-modulated interactions towards electrocatalysts and reveals the roles and effects on the metal nanoclusters for ORR/OER performance.