The invention relates to a method for preparing a multi-layer composite functional surgical dressing. The method comprises the following steps: respectively and independently carding the fiber layers comprising a functional layer which is formed by mixing chitosan fiber or chitosan fiber and viscose and is directly contacted with the skin, a water-absorbing layer which is made of viscose and has high liquid absorption performance and a protective layer which is formed by mixing the viscose and polyester fiber and has the supporting and protecting functions so as to form a net, manufacturing a three-layer laminate with an upper functional layer, a middle water-absorbing layer and a lower protective layer by employing a water jet strengthening technology, coating a waterproof agent on the protective layer of the three-layer laminate to form a waterproof layer, and finally rolling to obtain the surgical dressing. The product has high biocompatibility and promotes healing, the antibacterial rate is up to 96.7 percent, the liquid absorption rate is 1259 percent, the waterproofing grade is up to level 5, and the surgical dressing can be used for clinical repair for operative incision, burn, scald, ulcer and other skin injury and is simple in production process, low in cost and environmentally-friendly.