The invention discloses a method of preparing a zwitterionic membrane based on amphoteric silicon copolymer. The method comprises the following steps of selecting a monomer A containing a double bond and methyl halide, a monomer B containing a carboxyl, anhydride or sulfurous acid group and a monomer C containing a double bond and a silicon alkoxy group, mixing the three monomers, a solvent and an initiator, carrying out free radical copolymerization, and carrying out rotary evaporation concentration to obtain a silicon copolymer solution; and treating the silicon copolymer by two ammoniation modes, wherein one mode comprises the following steps of carrying out ammoniation on the silicon copolymer, and then mixing the silicon copolymer after ammoniation with polyvinyl alcohol (PVA), i.e. dropwise adding the silicon copolymer solution in a trimethylamine organic solution, then carrying out sol-gel reaction on the mixture and PVA, and carrying out heat treatment to form the zwitterionic membrane; and the other mode comprises the following steps of mixing the silicon copolymer and PVA, and then carrying out ammoniation on the mixture, i.e. directly dropwise adding the silicon copolymer solution in the PVA solution, then carrying out sol-gel reaction and heat treatment to form a membrane, selectively soaking the membrane with a trimethylamine aqueous solution, and then carrying out quaternization to obtain the zwitterionic membrane.