Room-temperature polar skyrmion bubbles that are recently found in oxide superlattice, have received enormous interests for their potential applications in nanoelectronics due to the nanometer size, emergent chirality, and negative capacitance. For practical applications, the ability to controllably manipulate them by using external stimuli is prerequisite. Here, we study the dynamics of individual polar skyrmion bubbles at the nanoscale by using in situ biasing in a scanning transmission electron microscope. The reversible electric field-driven phase transition between topological and trivial polar states are demonstrated. We create, erase and monitor the shrinkage and expansion of individual polar skyrmions. We find that their transition behaviors are substantially different from that of magnetic analogue. The underlying mechanism is discussed by combing with the phase-field simulations. The controllable manipulation of nanoscale polar skyrmions allows us to tune the dielectric permittivity at atomic scale and detailed knowledge of their phase transition behaviors provides fundamentals for their applications in nanoelectronics.