Fe-N-C materials exhibit excellent activity and stability for oxygen reduction reaction (ORR), as one of the most promising candidates to replace commercial Pt/C catalysts. However, it is challenging to unravel features of the superior ORR activity originating from Fe-N-C materials. In this work, the electronic and geometric structures of the isolated Fe-N-C sites and their correlations with the ORR performance are investigated by varying the secondary thermal activation temperature of a rationally designed NC-supported Fe single-atom catalyst (SAC). The systematic analyses demonstrate the significant role of coordinated atoms of SA and metallic Fe nanoparticles (NPs) in altering the electronic structure of isolated Fe-N-C sites. Meanwhile, strong interaction between isolated Fe-N-C sites and adjacent Fe NPs can change the geometric structure of isolated Fe-N-C sites. Theoretical calculations reveal that optimal regulation of the electronic and geometric structure of isolated Fe-N-C sites by the co-existence of Fe NPs narrows the energy barriers of the rate-limiting steps of ORR, resulting in outstanding ORR performance. This work not only provides the fundamental understanding of the underlying structure-activity relationship, but also sheds light on designing efficient Fe-N-C catalysts.