Bimetallic Janus nanostructures (JNs) have been revealed to be valuable materials because they have unique intermetallic interfaces that enable their potential use in a range of applications. However, with the increasing miniaturization of electronic devices, particle sizes influence the structure and orientation of these heterointerfaces, which plays a significant role in their application. Our in situ annealing experiments with high-resolution transmission electron microscopy have shown that for particle sizes in the sub-10 nm range, CuAg JNs preferentially show a Cu(100)/Ag(100) interface, differing from the larger CuAg JNs, where the Cu(111)/Ag(111) interface is favored. We discuss a feasible atomic motion mechanism to explain the effect of particle size on the formation of different heterointerfaces. Our results reveal the presence of a novel sub-10 nm heterostructure with a unique Cu(100)/Ag(100) interface and also provide crucial insights into understanding the role of particle size in interfacial evolution during thermal annealing of heterostructures.