The electronic structure, transport properties and magnetic properties of the material can be adjusted by regulating the formation and concentration of anionic vacancies. In particular, materials based on transition metal chulides (TMC) have high second-order nonlinearity and atomic thin thickness, and anionic vacancy engineering can effectively achieve the optimization of material properties. However, the impact of anion vacancy engineering on dipole polarization has not been fully resolved and clarified yet, and it cannot be solely relied upon semi-empirical methods. Therefore, it is of utmost importance to deeply understand the intrinsic mechanism between vacancies and electromagnetic (EM) parameters. This knowledge will provide crucial guidance for the development of advanced electromagnetic wave (EMW) absorption materials. In this study, a novel approach is proposed for the first time, which involves the creation of Se vacancies at the heterogeneous interface formed by Fe-Se compounds. Remarkably, the generation of Se vacancies leads to an increased electron transfer from Fe to Se atoms, resulting in the formation of numerous dipolarization centers. This effect significantly enhances the material’s polarization loss capacity. Furthermore, the presence of Se vacancies acts as traps for nearby free electrons, reducing the material’s conductivity, weakening the skin effect, and improving impedance matching. The precise modulation of Se vacancies in Fe-Se compounds has led to the achievement of ultrathin characteristics and significantly enhanced EM absorption capabilities. With a thickness of only 1.5 mm, the effective absorption bandwidth (EAB) reaches 5.42 GHz, covering the Ku band, which represents a remarkable increase of 53.5 % compared to unmodified Fe-Se compounds. At a thickness of 1.3 mm, the minimum reflection loss (RL) reaches −42.4 dB, demonstrating an impressive improvement of 41.3 %. Moreover, simulations of the radar cross section (RCS) indicate that the material possesses a robust microwave attenuation ability, underscoring its great potential for practical applications.