SnSe is a promising thermoelectric (TE) that has attracted increasing attention in recent years. Nano-engineering provides a straightforward and practical approach to enhancing the TE transport performance and mechanical strength of materials. This study reported a strategy that could effectively enhance the figure of merit (ZT) to 1.65 with an endotaxially nanostructured 0.5% telluride specimen. Additionally, this prominent performance was due to a closely coupled phonon-blocking/electron-transmitting approach through the embedding of endotaxially nanostructured second phases. The valence band alignment between the matrix SnSe and the embedded second-phase metal telluride (ATe, A = Pb, Ge, Ga, and Zn) controlled the hole transport by embedding a suitable forbidden band. Surprisingly, the nanostructured GaTe second phase with a broader energy gap compared to SnSe played a dual role of tuning the carrier concentration and holding the carrier mobility to increase the electrical transport properties to 710 μWcm–1K–2 and enhancing the phonon scattering, which decreased the lattice thermal conductivity ~ 0.2 Wm–1K–1 at 823 K. Finally, a peak ZT ~ 1.65 at 823 K and high mechanical properties were obtained. Consequently, these values could be more competitive in most reported polycrystalline SnSe materials and provided a favorable reference for the subsequent modifications, which showcased the potential of the SnSe-based nanocomposites fabricated in this study for cost-effective TE applications.