The invention relates to an allicin vaginal suppository and a preparation method thereof. The allicin vaginal suppository comprises following components in percentages by weight: allicin 0.2-5%, substrate 20-79%, emulsifier 0.01-1%, acetic acid 0.1-15%, chitosan 0.1-10%, and distilled water 1-30%; wherein the sum of the percentages of the components is 100%, the substrate adopts glycerin and gelatin, or adopts polyethyleneglycol substances, and the polyethyleneglycol substances includes at least one of polyethyleneglycol 400, polyethyleneglycol 1000, polyethyleneglycol 1500 and polyethyleneglycol 4000; the emulsifier adopts tween substances, and the tween substances includes at least one of tween-80, tween-60 and tween-40. The invention further provides the preparation method of the allicin vaginal suppository; according to the allicin vaginal suppository, the gynecological inflammation can be treated effectively, synchronously the organism immunity of patients can be enhanced, the use of drugs is improved, the administration frequency is reduced, and the use is convenient.