Rational synthesis of Pt−Au_n nanoparticles (NPs) has been achieved by overgrowing Au on Pt with n, the number of Pt−Au heterojunctions in each particle, controlled from 1 to 4, and the corresponding NPs in pear-, peanut-, or clover-like morphology. Monte Carlo simulation reveals that the morphology control can be correlated to a thermodynamic equilibrium of the Au coherence energy, the overall particle surface energy, and the heterogeneous Pt−Au interfacial energy in the composite system, which is manipulated by the seeding particle size and solvent polarity. The developed synthetic strategy together with the provided fundamental understanding of heterogeneous nucleation and heterostructure growth could have great potential toward the rational synthesis of composite nanomaterials with morphology control for advanced catalytic and other functional applications.