The invention belongs to the technical field of sugar making, and particularly relates to a method for preparing functional seasoning syrup through a biological fermentation method. The syrup is prepared from sugarcane juice, brown granulated sugar, brown sugar, galactose, yellow corn steep liquor, fructus cannabis pulp, sucrose mutase, fructosyl transferase, trehalose synthase, arabinose isomerase, flavor yeast and lysozyme; the materials are subjected to grading fermentation, filtration, lysozyme sterilization, concentration and other processes to prepare the seasoning syrup. The functionalseasoning syrup has multiple effects, and the problems that a seasoning sugar product in the market is monotonous in effect and has many side defects are effectively solved. The functional syrup is prepared through biological fermentation method, three prebiotic factors including isomaltitol, fructo-oligosaccharide and tagatose are generated through fermentation, and the product is endowed with the prebiotic functional factors. The biological preservative is used, and is safe and free of health risks; the product also overcomes the defects that after common syrup is used for cooking, dishes are hardened, viscous, likely to change colors and the like.