Heteroatoms-modified Fe–N–C catalysts have garnered significant attention for enhancing the oxygen reduction reaction (ORR). However, revealing the correlation between the type of heteroatoms used for doping and catalytic performance still faces significant challenges. Herein, based on the density functional theory (DFT), a series of heteroatom-modified Fe–N–C models with the tailored Fe–N4-X (X = S, P or B) site are constructed to explore the regulatory mechanism of heteroatoms on the electronic structure and adsorption behavior of Fe centers. Theoretical calculations reveal that the doping of S atoms can optimize the electronic environment of Fe atoms, thus leading the favorable interaction between Fe–N4–S site and OH intermediates. As a result, the Fe–N4–S site possess a lower energy barrier for the desorption of OH* than that of Fe–N4–B and Fe–N4–P, indicating higher catalytic activity and kinetics of S-modified Fe–N–C catalysts.