The invention discloses flute diaphragm glue and a manufacturing method thereof. The flute diaphragm glue comprises, by weight, 5-10 parts of donkey-hide gelatin powder, 3-6 parts of gellan gum, 14-32 parts of mucopolysaccharide, 0.2-2.2 parts of mucoprotein, 30-55 parts of deionized water and 10-20 parts of lysozyme. The manufacturing method of the flute diaphragm glue comprises 1, weighing 5-10 parts by weight of donkey-hide gelatin powder, 3-6 parts by weight of gellan gum, 14-32 parts by weight of mucopolysaccharide and 0.2-2.2 parts by weight of mucoprotein, crushing the above materials to obtain granules, pouring the granules into 30-55 parts by weight of deionized water and 10-20 parts by weight of lysozyme, putting all the raw materials into a container, and carrying out stirring at a rate of 800-900rpm to obtain a uniform mixture, and 2, covering the container with a cover, steaming the raw materials in the container for 2-3h until the raw materials form threads, pouring the melt raw material threads into a mold, carrying out cooling curing and packaging the finished product.