Bi₂Te₃-based alloys have been long regarded as the materials chosen for room temperature thermoelectric (TE) applications. With superior TE performances, Bi₂Te₃-based bulk materials have been commercially used to fabricate TE devices already. However, bulk materials are less suitable for the requirements for applications of flexible or thin film TE devices, and therefore the thin film materials with advanced TE properties are highly demanded. Comparing with bulk materials and P-type Bi₂Te₃-based thin films, the TE properties of N-type Bi₂Te₃-based thin films have been relatively poor so far and need further improving for practical applications. In this study, a series of N-type Bi₂Te_3–xSe_x thin films is prepared via magnetron sputtering method, and their structures can be precisely controlled by adjusting the sputtering conditions. Preferential layered growth of the Bi₂Te_3–xSe_x thin films along the (00l) direction is achieved by adjusting the substrate temperature and working pressure. Superior electrical conductivity over 10⁵ S/m is achieved by virtue of high in-plane mobility. combining the advanced Seebeck coefficient of Bi₂Te₃-based material with superior electrical conductivity of highly oriented Bi₂Te_3–xSe_x thin film, a high power factor (PF) of the optimal Bi₂Te_3–xSe_x thin film can be enhanced to 42.5 μW/(cm·K²) at room temperature, which is comparable to that of P-type Bi₂Te₃-based thin film and bulk material.