The exploitation of nanoconfined conversion of Au- and Pt-containing binary nanocrystals for developing a controllable synthesis of surfactant-free AuPt nanocrystals with enhanced formic acid oxidation (FAO) activity is reported, which can be stably and evenly immobilized on various support materials to diversify and optimize their electrocatalytic performance. In this study, an atomic layer of Pt2+ species is discovered to be spontaneously deposited in situ on the Au nanocrystal generated from a reverse-microemulsion solution. The resulting Au/Pt2+ nanocrystal thermally transforms into a reduced AuPt alloy nanocrystal during the subsequent solid-state conversion process within the SiO2 nanosphere. The alloy nanocrystals can be isolated from SiO2 in a surfactant-free form and then dispersedly loaded on the carbon sphere surface, allowing for the production of a supported electrocatalyst that exhibits much higher FAO activity than commercial Pt/C catalysts. Furthermore, by involving Fe3O4 nanocrystals in the conversion process, the AuPt alloy nanocrystals can be grown on the oxide surface, improving the durability of supported metal catalysts, and then uniformly loaded on a reduced graphene oxide (RGO) layer with high electroconductivity. This produces electrocatalytic AuPt/Fe3O4/RGO nanocomposites whose catalyst-oxide-graphene triple-junction structure provides improved electrocatalytic properties in terms of both activity and durability in catalyzing FAO.