AbstractInversion symmetry breaking is critical for many quantum effects and fundamental for spin‐orbit torque, which is crucial for next‐generation spintronics. Recently, a novel type of gigantic intrinsic spin‐orbit torque is established in the topological van der Waals (vdW) magnet iron germanium telluride. However, it remains a puzzle because no clear evidence exists for interlayer inversion symmetry breaking. Here, the definitive evidence of broken inversion symmetry in iron germanium telluride directly measured by the second harmonic generation (SHG) technique is reported. The data show that the crystal symmetry reduces from centrosymmetric P6₃/mmc to noncentrosymmetric polar P3m1 space group, giving the threefold SHG pattern with dominant out‐of‐plane polarization. Additionally, the SHG response evolves from an isotropic pattern to a sharp threefold symmetry upon increasing Fe deficiency, mainly due to the transition from random defects to ordered Fe vacancies. Such SHG response is robust against temperature, ensuring unaltered crystalline symmetries above and below the ferromagnetic transition temperature. These findings add crucial new information to the understanding of this interesting vdW metal, iron germanium telluride: band topology, intrinsic spin‐orbit torque, and topological vdW polar metal states.