The present invention provides functional rare sugar syrup and a preparation method thereof. A mass percentage of sucrose syrup in the rare sugar syrup is 0-99%. The rare sugar syrup is one or more of trehalose syrup, fructooligosaccharide syrup, allulose syrup, arabinose syrup, meso-erythritol syrup, neohesperidin dihydrochalcone syrup, stevioside syrup, maltooligosaccharide syrup, isomaltooligosaccharide syrup, galacto-oligosaccharide syrup, soybean oligosaccharide syrup, mixed cottonseed sugar, lactose and sucrose syrup, xylo-oligosaccharide syrup, mannan-oligosaccharide syrup, cyclodextrin glucose syrup, gentiobiose syrup, coupling sugar syrup, panose syrup, milk oligosaccharide syrup, chitin oligosaccharide acetylglucosamine syrup and ganoderma lucidum polysaccharide syrup. The functional rare sugar syrup has functions of protecting cells, regulating flora balance in body, regulating balances of blood sugar, blood pressure and blood lipids, protecting internal organs, promoting absorption of nutrients, preventing obesity, dental caries, oxidation and tumors, delaying aging, etc.