• A novel MXene@S-deficient ZnIn 2 S 4 heterostructure is designed for electromagnetic wave absorbing material. • The unique synthetic effects of interfacial and vacancy engineering can efficiently enhance electromagnetic wave absorbing ability. • The MXene@S-deficient ZnIn 2 S 4 also exhibits antibacterial ability for endowing its multi-function application potential. Interface and vacancy engineering on electromagnetic absorbing materials have been proved to be two effective strategies to enhance electromagnetic absorbing performance. Herein, a Ti 3 C 2 T x MXene/ZnIn 2 S 4 heterostructure with tunable interface/vacancy structure is fabricated, and the controllable electromagnetic properties are realized by the dual optimization. The intercalated nano-interface design of MXene is realized via the ultrathin 2D nanosheet structure of ZnIn 2 S 4 , and the vacancy structure design is realized by regulating the concentration of S vacancies. Benefiting from the synergistic effect of interface/vacancy dual optimization, the band structure and electron transport of the heterostructure are adapted, and the interface and dipolar polarization effect are improved. The effective absorption bandwidth of the heterostructure reaches 4.8 GHz (∼1.5 mm) with a minimum reflection loss of -38.5 dB. The results show that reasonable interface and vacancy structure design can not only affect the conductive loss by adjusting the energy gap but also improve the polarization loss through the interfacial and dipolar polarization. In addition, the interaction between MXene and ZnIn 2 S 4 also promotes carrier migration, which makes the heterostructure exhibit strong antibacterial activity. This interface/vacancy dual optimization approach provides a valuable direction for the development of multifunctional electromagnetic absorption materials in the field of multi-functional devices.