The invention discloses a multifunctional active frequency selective surface and a control method thereof. The active frequency selective surface comprises a dielectric substrate and two metal periodic arrays arranged orthogonally on the upper side and lower side of the dielectric substrate; each metal periodic array comprises a plurality of metal units in periodic array distribution; and each metal unit is square and includes two metal thin wire structures, two metal thick wire structures and a PIN diode. When the multifunctional active frequency selective surface works, direct-current bias voltage excitation is applied to the upper-layer metal periodic array and the lower-layer metal periodic array so as to carry out encoding; and one of an electromagnetic switch function and a polarization selection function can be realized by changing encoding states, so that the multi-functional active frequency selective surface can be in a double-polarized band-pass state, a double-polarized shielding state, a TE polarized wave selection state or a TM polarized wave selection state. The multifunctional active frequency selective surface of the invention integrates many functions, is simple in manufacture, has good angle stability, can actively control electromagnetic waves and has a bright application prospect.