The invention provides a preparation method of a compound double-layer sustained release emulsion for treating diseases of oral mucosa made from the following raw materials: borneol, calculus bovis artifactus, tindazole tinidazole, dyclonine hydrochloride, Tween-80, glycerol, saccharin sodium, sodium carboxymethyl cellulose (CMC-Na), polyvinyl alcohol PVA17-18 etc. The compound double-layer sustained release emulsion has heat-cleaning and detoxifying, swelling-dispersing and ache-relieving, bacteria-resisting and inflammation-diminishing, putridity-impelling and tissue regeneration-promoting, ulcer face and lesion place-effectively protecting and curing functions, shortens course of the disease, overcomes deficiencies of single-layer emulsion of Chinese medicine or western medicine, is durable with obvious curative effect. When a double-layer emulsion is compared with a single-layer emulsion, medicine is released from a single layer in the single-layer emulsion and from double layers in the double-layer emulsion, thus medicine locally contacts the lesion places, the medicine flowing outside is decreased and foreign odour of medicine in oral cavity is decreased. The compound double-layer sustained release emulsion is made by combining advantages of Chinese medicine and western medicine which are rationally matched, has low dosage, direct effect, convenient use, quick effect, low side effect, determined and good curative effect.