Oriented n-type bismuth telluride thin films with various layered nanostructures have been fabricated by radio-frequency (RF) magnetron sputtering. The crystal structures and microstructures of the films were characterized by X-ray diffraction (XRD) and scanning electron microscopy (SEM), respectively. The transport properties including carrier concentration, mobility, Seebeck coefficient and in-plane electrical conductivity were measured, which showed strong microstructure-dependent behaviors. The relationship between morphologies and transport properties of the films was explored. The optimal morphology and transport properties of films were obtained at the substrate temperature of 350 °C under the pressure of 1.0 Pa with oriented layered structure. Based on these results, a formation mechanism of these nanostructures is proposed and discussed. The interfaces and grain boundaries formed in these layered structures are beneficial to the reduction in thermal conductivity, which could result in potential TE films with high ZT value.