Modulation of the local electronic structure of isolated coordination structures plays a critical role in electrocatalysis yet remains a grand challenge. Herein, we have achieved electron perturbation for the isolated iron coordination structure via tuning the iron spin state from a high spin state (FeN4) to a medium state (FeN2B2). The transition of spin polarization facilitates electron penetration into the antibonding π orbitals of nitrogen and effectively activates nitrogen molecules, thereby achieving an ammonia yield of 115 μg h–1 mg–1cat. and a Faradaic efficiency of 24.8%. In situ spectroscopic studies and theoretical calculations indicate that boron coordinate sites, as electron acceptors, can regulate the adsorption energy of NxHy intermediates on the Fe center. FeN2B2 sites favor the NNH* intermediate formation and reduce the energy barrier of rate-determining steps, thus accounting for excellent nitrogen fixation performance. Our strategy provides an effective approach for designing efficient electrocatalysts via precise electronic perturbation.