Phase change memory (PCM) is a leading candidate for nonvolatile memory applications in the big data era. However, the high power consumption, caused by melting GeTe-Sb2Te3-like phase change materials, hinders their applications. A significant step is the proposal to spatially separate GeTe and Sb2Te3 in the form of a superlattice, enabling a higher operating speed and better cyclability at reduced switching energy. However, the physical origin is under intensive debate. Recently, the swapping of the SbTe terminating layers nearest to the van der Waals (vdWs) gap has been claimed to be the mechanism for the superlattice. Here, we reported a direct atomic-scale chemical identification of two kinds of vdWs reconfigurations together with atomic simulations. The vdWs reconfigurations, which occurred at the GeTe and Sb2Te3 boundary, were demonstrated to change the electrical properties and turn this semiconductor into a conductor, leading to the resistance contrast. Besides, strong intermixing of Ge and Sb atoms was directly observed; in the most severe cases, ∼50% of Ge in the GeTe layer diffused into the adjacent Sb2Te3 layer. Our work paves the way for deeper understanding of the phase transition of the GeTe/Sb2Te3 superlattice and the future design of non-volatile memories towards dynamic random access-like memories.