Topological polar structures, in analogy to spin vortices and skyrmions, have received tremendous attention for their fascinating prospects in future device applications. However, in the widely studied ferroelectric-based superlattices, the epitaxial heterointerfaces, yielding desired strain, depolarization, and gradient energies, greatly confine the mobility of the topological solitons. Here, we report observation of polar vortex–antivortex pairs near junctions of antiphase boundaries in antiferroelectric PbZrO3 thin films by using atomic-resolution scanning transmission electron microscopy. Our temporal-resolved lattice analysis reveals that the local strain gradient caused by an incommensurate modulation constructs the smallest topological units reported to date. Our phase-field simulations unveil that the Pb–O vacancy-induced random electric fields account for their three-dimensional formation, and the stimulus of electron-beam irradiation can drive their dynamic migration. The findings offer a new approach to comprehend fundamental physics about antiferroelectricity and the design of functional devices based on topological structures in antiferroelectric thin films.