Electron microscopy has evolved from a passive imaging tool into an active probe capable of modifying intrinsic material properties. While electron beam-induced polarization control is well established in conventional ferroelectric oxides, its impact on van der Waals (vdW) ferroelectrics remains unexplored. Here, we demonstrate that vdW ferroelectric CuInP2S6 (CIPS), exhibiting sextuple intrinsic polarization states, is exceptionally responsive to ultralow-energy electron beam irradiation. Using an accelerating voltage as small as 0.5 kV, we achieve unidirectional polarization switching driven by localized electric fields generated from surface charge accumulation and uniformization of piezoresponse amplitudes crossing all domains, indicating reconfigured ferroelectric-antiferroelectric states. Notably, electron beam exposure also induces local morphological protrusions accompanied by unique circular domain textures, which can be attributed to a ferroelectric phase transition triggered by the collective migration of Cu+ ions across vdW gaps toward the surface. These findings offer valuable insights into noncontact electron-beam-driven polarization reconfiguration and ionic conduction in vdW ferroionic systems.