The invention discloses an antibacterial peptide hand sanitizer and a preparation method thereof. The antibacterial peptide hand sanitizer consists of ingredients of antibacterial peptide, decontaminant, stabilizing agent, plant extract and the like, and concretely consists of the ingredients, by weight part, 1-5 parts of the antibacterial peptide, 0.05-0.2 part of kathon, 5-10 parts of the decontaminant which is ammonium laureth sulfate, 3-10 parts of moisturizing and skin protecting agent which is glycerol, 3-8 parts of conditioning agent which is citric acid, 2-6 parts of the stabilizing agent which is coconut fatty acid diethanol amine, 10-20 parts of the plant extract and 100 parts of the balance deionized water. The antibacterial peptide hand sanitizer is remarkable in bacterium inhibition and decontamination function, has multiple effects of protecting skin and the like, and is convenient to prepare.