The invention discloses a preparation method of a mulberry residue extract microcapsule applied to baked biscuits, which comprises the following steps: carrying out biological enzyme method coupled ultrasonic-assisted extraction on mulberry residue byproducts left after juicing in a factory to obtain a mulberry residue polyphenol extracting solution; purifying the mulberry residue extracting solution, and performing vacuum concentration for later use; fermenting the litchi pomace with lactobacillus casei to obtain fermented litchi pomace; homogenizing and uniformly mixing the mulberry pomace extracting solution and the fermented litchi pomace; and carrying out freeze spray drying on the mixed materials to obtain the mulberry residue extract microcapsules. By extracting mulberry residues, and purifying and concentrating the extracting solution, the functional components in mulberry residues are fully extracted, the mulberry residue extracting solution and the fermented litchi pomace aresubjected to freeze drying through vacuum freeze drying, the capsules are prepared, the stability of polyphenol compounds is guaranteed, the functional bakery products such as biscuit and bread are convenient to make and use, and the method has good economic and social benefits.