Intermetallic nanoparticles (iNPs) have yielded enormous successes in catalytic applications by the formation of ordered phases. However, atomic level understanding of the alloying mechanism, which plays a pivotal role for controlling intermetallic phases and tailoring their catalytic properties, is still elusive. In this study, we discovered a consecutive formation of ordered Pt3Sn and PtSn phases during the growth of Pt–Sn iNP inside a well-defined nano-reactor at elevated temperature using in-situ scanning transmission electron microscopy. We found that the surface-mediated diffusion of Sn controls overall dynamics of the reaction, while the unique coherent interfacial structure is determinative for the PtSn transformation. We then further controlled the phase selection of Pt–Sn iNPs and demonstrated their distinguishable catalytic behaviors. Our findings not only provide detailed experimental evidence on the alloying mechanism in intermetallic nanoscale systems, but also pave the way for mechanistic control of synthesis and catalytic properties of iNPs.