Pt-based intermetallic nanostructures have demonstrated higher electrocatalytic performances compared to random alloy structures. However, the origin of their enhanced catalytic properties remains elusive. Furthermore, a robust synthetic strategy for well-defined intermetallic nanostructures represents a challenge. Here, we reveal by combining theoretical and experimental results that the activity enhancement in intermetallic structures for the oxygen reduction reaction (ORR) originates from an intensified ligand effect. We prepared well-defined model nanocatalysts via confined nanospace-directed synthesis using mesoporous silica templates, which allows precise control over the size and shape of nanostructures. Importantly, this method can transform disordered alloy nanostructures into intermetallic analogues without agglomeration, enabling decoupling of an atomic ordering effect in catalysis. The prepared ordered intermetallic Pt3Co nanowires (O-Pt3Co NWs) can benefit from an intensified ligand effect, Pt-skin layer, and agglomeration-tolerant contiguous structure, which led to their enhanced ORR activity and durability compared to disordered alloy Pt3Co nanowires (D-Pt3Co NWs) and Pt/C catalysts. The multifunctionality of O-Pt3Co NWs is demonstrated with their higher activity and durability in the alkaline hydrogen evolution reaction and acidic methanol oxidation reaction than those of D-Pt3Co NWs and Pt/C catalysts. Furthermore, a proton exchange membrane fuel cell cathode based on O-Pt3Co NWs shows much better durability than a Pt/C-based one.