Designing atomically dispersed metal catalysts for oxygen reduction reaction (ORR) is a promising approach to achieve efficient energy conversion. Herein, we develop a template-assisted method to synthesize a series of single metal atoms anchored on porous N,S-codoped carbon (NSC) matrix as highly efficient ORR catalysts to investigate the correlation between the structure and their catalytic performance. The structure analysis indicates that an identical synthesis method results in distinguished structural differences between Fe-centered single-atom catalyst (Fe-SAs/NSC) and Co-centered/Ni-centered single-atom catalysts (Co-SAs/NSC and Ni-SAs/NSC) because of the different trends of each metal ion in forming a complex with the N,S-containing precursor during the initial synthesis process. The Fe-SAs/NSC mainly consists of a well-dispersed FeN4S2 center site where S atoms form bonds with the N atoms. The S atoms in Co-SAs/NSC and Ni-SAs/NSC, on the other hand, form metal-S bonds, resulting in CoN3S1 and NiN3S1 center sites. Density functional theory (DFT) reveals that the FeN4S2 center site is more active than the CoN3S1 and NiN3S1 sites, due to the higher charge density, lower energy barriers of the intermediates, and products involved. The experimental results indicate that all three single-atom catalysts could contribute high ORR electrochemical performances, while Fe-SAs/NSC exhibits the highest of all, which is even better than commercial Pt/C. Furthermore, Fe-SAs/NSC also displays high methanol tolerance as compared to commercial Pt/C and high stability up to 5000 cycles. This work provides insights into the rational design of the definitive structure of single-atom catalysts with tunable electrocatalytic activities for efficient energy conversion.