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Abstract Thermoelectric multilayer thin films used in nanoscale energy conversion have been receiving increasing attention in both academic research and industrial applications. Thermal transport across multilayer interface plays a key role in improving thermoelectric conversion efficiency. In this study, the cross-plane thermal conductivities of nano-constructed Sb2Te3/(Cu, Ag, Au, Pt) thermoelectric multilayer thin films have been measured using time-domain thermoreflectance method. The interface morphology features of multilayer thin film samples were characterized by using scanning and transmission electron microscopes. The effects of interface microstructure on the cross-plane thermal conductivities of the multilayer thin films have been extensively examined and the thermal transfer mechanism has been explored. The results indicated that electron–phonon coupling occurred at the semiconductor/metal interface that strongly affected the cross-plane thermal conductivity. By appropriately optimizing the period thickness of the metal layer, the cross-plane thermal conductivity can be effectively reduced, thereby improving the thermoelectric conversion efficiency. This work presents both experimental and theoretical understanding of the thermal transport properties of Sb2Te3/metal multilayer thin film junctions with important implications for exploring a novel approach to improving the thermoelectric conversion efficiency.