The invention discloses a bee venom antimicrobial preparation and a preparation method thereof. The bee venom antimicrobial preparation is prepared from, by weight, 15-25% of chlorhexidine acetate, 5-10% of a bee venom source solution, 0.7-1.5% of a red date extracting solution, 0.2-0.5% of a rose flower extracting solution, 0.4-0.6% of a honeysuckle flower extracting solution, 0.3-0.8% of vanillyl butyl ether, 0.7-0.9% of propylene glycol and 50-70% of purified water. Accordingly, related symptoms caused by meridian obstruction are relieved, and good inhibiting and killing effects on germs and inflammations of the surface of the skin are achieved; by adding the rose flower extracting solution, the probability that a user has allergy can be effectively lowered, the immune function of the user is improved, and the disease resistance is enhanced; by adding the honeysuckle extracting solution, the certain inhibiting effect can be achieved on staphylococcus aureus, hemolytic streptococcus,escherichia coli, shigella dysenteriae, vibrio cholera, typhoid bacilli, salmonella paratyphi and the like.