As an important aspect of crystal phase engineering, controlled crystal phase transformation of noble metal nanomaterials has emerged as an effective strategy to explore novel crystal phases of nanomaterials. In particular, it is of significant importance to observe the transformation pathway and reveal the transformation mechanism in situ. Here, the phase transformation behavior of face‐centered cubic (fcc) Au nanoparticles (fcc‐AuNPs), adhering to the surface of 4H nanodomains in 4H/fcc Au nanorods, referred to as 4H‐AuNDs, during in situ transmission electron microscopy imaging is systematically studied. It is found that the phase transformation is dependent on the ratio of the size of the monocrystalline nanoparticle (NP) to the diameter of 4H‐AuND. Furthermore, molecular dynamics simulation and theoretical modeling are used to explain the experimental results, giving a size‐dependent phase transformation diagram which provides a general guidance to predict the phase transformation pathway between fcc and 4H Au nanomaterials. Impressively, this method is general, which is used to study the phase transformation of other metal NPs, such as Pd, Ag, and PtPdAg, adhering to 4H‐AuNDs. The work opens an avenue for selective phase engineering of nanomaterials which may possess unique physicochemical properties and promising applications.