The dynamics of oxygen vacancies under external stimuli dominates the performance of many solid-state devices, including capacitors, oxide memristors, anionic conductors, etc. By means of in situ transmission electron microscopy, it is found in BaTiO 3 perovskite nanocrystals that formation of oxygen vacancies due to electrical stressing renders the oxide amorphizable under electron beam illumination, suggesting the presence of a threshold concentration of oxygen vacancy affecting the structural stability of BaTiO 3 crystals upon high energy radiation. In contrast to the structural change, the resistivity of the nanocrystal seems not liable to the amorphization prior to dielectric breakdown at higher voltage bias. It is proposed that an increase in oxygen vacancy content promotes oxygen mobility in the perovskite structure allowing electron beam induced electric field to modify the local structure and composition. The in situ observations reveal the central role of oxygen vacancies in the structural stability of perovskites which is of paramount importance to their applications in extreme environments and suggest a potential new route to micro-processing perovskite oxides using the electron beam via oxygen vacancy management without severely compromising the electric property.