Based on density functional perturbation theory, phonon properties and electron-phonon interaction in Bi₄Se₃ film system are studied with first-principles calculations. It shows that dynamic of Bi₄Se₃ film system for two terminations is stable. There exists mismatch in projected phonon density of states between Bi₂ bilayer and Bi₂Se₃quintuple layer. It prevents part phonons to transport in Bi₄Se₃ film, which leads to thermal conductivity reduce and improves thermoelectric performance of material. Besides, electron-phonon coupling constant of Bi₄Se₃ film in two kinds of termination are small (about 0.278), which is in favour of electronic device in room temperature.