The invention discloses a longan proteoglycan which is prepared by the following method: selecting a longan flesh aqueous extract, and processing the longan flesh aqueous extract by using D301-F anion exchange resin to remove most proteins and pigments, thereby obtaining crude longan polysaccharide; separating and purifying the crude longan polysaccharide by using DEAE-52 cellulose ion exchange chromatographic columns, and eluting; and collecting the longan proteoglycan eluent, dialyzing, concentrating, and carrying out vacuum freeze drying to obtain longan proteoglycan powder. The invention also discloses a preparation method and application of the longan proteoglycan. The longan proteoglycan has the advantages of high yield and high purity. The preparation method of the longan proteoglycan can be used for carrying out deep processing on the longan product.