Carrier transport engineering in bulk semiconductors using inclusion phases often results in the deterioration of carrier mobility (μ) owing to enhanced carrier scattering at phase boundaries. Here, we show by leveraging the temperature-induced structural transition between the α-Cu2Se and β-Cu2Se polymorphs that the incorporation of Cu4TiSe4 inclusions within the Cu2Se matrix results in a gradual large drop in the carrier mobility at temperatures below 400 K (α-Cu2Se), whereas the carrier mobility remains unchanged at higher temperatures, where the β-Cu2Se polymorph dominates. The sharp discrepancy in the electronic transport within the α-Cu2Se and β-Cu2Se matrices is associated with the formation of incoherent α-Cu2Se/Cu4TiSe4 interfaces, owing to the difference in their atomic structures and lattice parameters, which results in enhanced carrier scattering. In contrast, the similarity of the Se sublattices between β-Cu2Se and Cu4TiSe4 gives rise to coherent phase boundaries and good band alignment, which promote carrier transport across the interfaces. Interestingly, the different cation arrangements in Cu4TiSe4 and β-Cu2Se contribute to enhanced phonon scattering at the interfaces, which leads to a reduction in the lattice thermal conductivity. The large reduction in the total thermal conductivity while preserving the high power factor of β-Cu2Se in the (1-x)Cu2Se/(x)Cu4TiSe4 composites results in an improved ZT of 1.2 at 850 K, with an average ZT of 0.84 (500-850 K) for the composite with x = 0.01. This work highlights the importance of structural similarity between the matrix and inclusions when designing thermoelectric materials with improved energy conversion efficiency.