In the present work, GeTe and Sb2Te3 van der Waals bonded superlattices epitaxially grown by molecular beam epitaxy are investigated. These structures are grown on passivated Si substrates, resulting in one single epitaxial domain and its twinned domain, both sharing the same out-of-plane orientation. Supported by X-ray diffraction and Raman spectroscopy, attention is called to the thermodynamically driven tendency of GeTe and Sb2Te3 to intermix into a Ge–Sb–Te (GST) alloy at the interfaces. A growth model is proposed to explain how these GST structures are formed.