The invention discloses an anti-bacterial high-viscosity medical glue, which is prepared from the following ingredients: 2-cyano-acrylate isopropyl, polyisoprene, polypropylene, povidone iodine, magnesium sulfate, naringenin, halloysitum rubrum nano-powder, vitamin A palmitate, plant essential oil, paraffins, alginate, disodium EDTA, methacrylamide, polyvinyl alcohol, dioctyl phthalate, 1.5g/ml luffa extract, 0.8g/ml rhizoma bletillae extract, glycerol and sterile water. The invention further discloses a preparation method of the anti-bacterial high-viscosity medical glue. The adhesive strength and 48-hour compressive strength of the medical glue are in a relatively high level, the medical glue is high in anti-bacterial ratio, short in hemostasis time, high in overall healing efficiency, free from irritation on wound tissues and excellent in overall performance, and conforms to the application requirements of clinics for the medical glue.