Pt-based catalysts are the most promising catalysts for proton exchange membrane fuel cells (PEMFCs) but still suffer from sluggish kinetics for the oxygen reduction reaction (ORR). Alloying Pt with transition-metal (M) elements is an efficient approach to modulate the electronic structure of Pt-based catalysts and improve the catalytic performance for the ORR. However, owing to the distinguishing surface state caused by different synthetic approaches, there still exist contradictory views about the relationship between the structure of Pt-based alloys and the catalytic performance for the ORR. In this work, PtCo alloys with a similar surface state but diverse structures and compositions are obtained by regulating the annealing temperatures and the precursor ratios. Accompanied by the structure and composition evolution, the electronic structure of Pt has also changed. PtCo@sOMC-900-1/3 with the intermetallic compound structure achieves the best kinetic activity as well as durability, indicating its potential for practical application. This work provides a more accurate understanding of the relationship between the alloy structure and the catalytic ORR performance and highlights a feasible strategy to mass-produce cathode catalysts for PEMFC applications.