<p>The topological surface states (TSS) of 3D topological insulators (TI) play a crucial role in their transport. How to avoid intrinsic defects in materials and thus increase the proportion of surface states in the transport process poses a great challenge to materials scientists. In our work, high-quality epitaxial topological insulator Bi₂Te₃ ultrathin films with flat surface were prepared by pulsed laser deposition (PLD). The insulating resistivity-temperature (<i>ρ</i>-<i>T</i>) curve in Bi₂(Te_xSe_1-x)₃ films with optimal doping concentration (25–35%) shows the transport of bulk state caused by intrinsic defects which is gradually suppressed. In thinner Bi₂Te₃ films, the <i>ρ</i>-<i>T</i> curve displays a transition from negative to positive slope at higher temperatures, which is attributed to enhanced electron–electron interaction (EEI). The transition from a parabolic to a linear to a weak anti-localization (WAL) was observed in the magnetoresistance (MR) results of pure Bi₂Te₃ ultrathin films with different thicknesses. By comparing the MR of Bi₂(Te_xSe_1-x)₃ films with different Se doping concentrations, it is found that the MR of the Se-doped films and the WAL near the zero magnetic field are obvious, and the change is greatest at the optimal doping concentration. The magnetoconductivity (MC) data ΔG can be fitted well by the quantum interference model Hikami, Larkin, and Nagaoka (HLN) equation at magnetic fields as high as ± 7&#xa0;T. This provides guidance for further research on how to enhance the TSS transport of 3D TIs.</p> Graphical Abstract <p></p>