Since the theoretical prediction of the existence of the topological insulating phase, ZrTe₅ has attracted a lot of interests in its topological nature, which may lead to the low-energy transport edge channels and the quantum spin Hall (QSH) effect in its two-dimensional form. Possible strain or photon induced topological transition from the topological insulator (TI) to the Dirac semimetal in ZrTe₅ has been recently suggested by experiments. Due to the layered structure of ZrTe₅, the van der Waals (vdW) interaction becomes an essential factor to study atomic vibrational behavior in the topological transition. In this theoretical work, phonon vibration modes and the corresponding electron band structures are explored systematically without and with vdW force correction to reveal the microscopic mechanism of the phase transition in ZrTe₅.