Pt-based multimetallic nanocrystals (NCs) have attracted tremendous research interest because of their excellent catalytic properties in various electrocatalysis fields. However, the development of rational synthesis approaches that can give multimetallic NCs with desirable compositional structures is still a radical issue. In the present work, we devised an efficient strategy for the systematic control of the spatial distribution of constituent elements in Pt-based trimetallic core-shell NCs, through which NCs with distinctly different compositional structures, such as Au@PdPt, Au@Pd@Pt, AuPd@Pt, and AuPdPt@Pt core-shell NCs, could selectively be generated. The adjustment of the amount of a reducing agent, hydrazine, which can provide control over the relative reduction kinetics of multiple metals, is the key to the selective formation of NCs. Through extensive studies on the effect of the compositional structure of the trimetallic NCs on their catalytic function toward the methanol electro-oxidation reaction, we found that the Au@Pd@Pt NCs exhibited considerably enhanced catalytic performance in comparison to the other trimetallic NCs as well as to their binary counterparts, a commercial catalyst, and reported Pt-based nanocatalysts due to the optimized surface electronic structure. The present strategy will be useful to design and construct multicomponent catalytic systems for various energy and environmental applications.