The invention discloses a preparation method of a high-efficiency compound antibacterial separation membrane, comprising the following steps: (1) preparing a membrane forming polymer and additive into membrane casting liquid, and adopting an immersion precipitation phase conversion method to prepare a polymer separation membrane; (2) carrying out annealing treatment on the polymer separation membrane; (3) successively dipping the annealing treatment polymer separation membrane into silver nitrate aqueous solution and sodium borohydride aqueous solution to obtain a polymer separation membrane the surface of which adsorbs silver nano particles; (4) dipping the polymer separation membrane the surface of which adsorbs the silver nano particles into crosslinker solution; carrying out quaternization and in situ crosslinking reaction; and drying to obtain the compound antibacterial separation membrane. The method is easy and simple to realize, and the prepared compound antibacterial separation membrane is stable and durable and has high antibacterial efficiency and obvious antibacterial effect.