Introducing nanoscale heterostructure interfaces into material matrix is an effective strategy to optimize the thermoelectric performance by energy-dependent carrier filtering effect. In this study, highly (00l)-oriented Bi2Te3/Te heterostructure thin films have been fabricated on single-crystal MgO substrates using a facile magnetron co-sputtering method. Bi2Te3/Te heterostructure thin films with Te contents of 63.8 at% show an optimized thermoelectric performance, which possess a Seebeck coefficient of -157.7 μV K-1 and an electrical conductivity of 9.72 × 104 S m-1, leading to a high power factor approaching 25 μW cm-1 K-2. The partially decoupled behavior of the Seebeck coefficient and electrical conductivity is contributed to Bi2Te3/Te heterostructure interfaces, which causes interfacial barrier filtering and scattering effects; thus, a high level of the Seebeck coefficient is obtained. Meanwhile, carrier transport in a-b plane can benefit from the highly preferred orientation, which guarantees a remarkably high electrical conductivity. We anticipate that our strategy may guide the way for preparing high-performance thermoelectric materials by microstructure design and regulation.