The dynamics of itinerant electrons in topological insulator (TI) thin films is investigated using a multi-band decomposition approach. We show that the electron trajectory in the 2D film is anisotropic and confined within a characteristic region. Remarkably, the confinement and anisotropy of the electron trajectory are associated with the topological phase transition of the TI system, which can be controlled by tuning the film thickness and/or applying an in-plane magnetic field. Moreover, persistent electron wavepacket oscillation can be achieved in the TI thin film system at the phase transition point, which may assist in the experimental detection of the jitter motion (Zitterbewegung). The implications of the microscopic picture of electron motion in explaining other transport-related effects, e.g., electron-mediated RKKY coupling in the TI thin film system, are also discussed.