The invention belongs to the technical field of fermentation of feeds, enzymic preparations and microorganisms and in particular relates to a preparation method of a fish meal small peptide feed. The preparation method of the fish meal small peptide feed comprises the following steps: mixing commercially-available poor-quality fish meal, molasses, brown sugar or glucose, water, microorganism protease, lactic acid bacteria strain liquid and saccharomycetes strain liquid to prepare a liquid fermentation culture medium, carrying out primary liquid fermentation and enzymolysis for 2-120 hours at the temperature being 20-70 DEG C to prepare fish meal small peptide liquid; mixing the fish meal small peptide liquid, corn flour and alfalfa powder to prepare a solid fermentation culture medium, carrying out secondary solid fermentation and enzymolysis for 6-360 hours at the temperature being 10-50 DEG C to prepare the fish meal small peptide feed. The prepared fish meal small peptide feed is capable of removing anti-nutritional factors, killing pathogenic microorganisms, producing abundant small peptides, lactic acid, yeast protein and probiotics, removing odor, presenting fishy sourness, improving the feed intake of livestock and poultry, promoting growth of piglets and improving milk yield of milking sows.