Superlattices consisting of stacked nano-sized GeTe and Sb2Te3 blocks have attracted considerable attention owing to their potential for an efficient non-melting switching mechanism, associated with complex bonding between blocks. Here, we propose possible atomic models for the superlattices, characterized by different interfacial bonding types. Based on interplanar distances extracted from ab initio calculations and electron diffraction measurements, we reveal possible intercalation of dangling bonds as the GeTe content in the superlattice increases. The dangling bonds were further confirmed by X-ray photoelectron spectroscopy, anisotropic temperature dependent resistivity measurements down to 2 K and magnetotransport analysis. Changes of partially coherent decoupled topological surfaces states upon dangling bonds varying contributed to the switching mechanism. Furthermore, the topological surface states controlled by changing the bonding between stacking blocks may be optimized for multi-functional applications.