The invention relates to a method for producing small peptide amino acid microelement chelate by way of the acid hydrolysis of protein. Animal protein or vegetable protein is adopted as raw material, and is hydrolyzed by hydrochloric acid. Hydrolysate is subjected to rough filtration and microfiltration, filtrate is deacidified by a nanofiltration membrane separation system, and the deacidified liquor is purified by way of ultrafiltration separation. Obtained small peptide and amino acid, the molecular weight of which is less than 1000 Dalton, are chelated with microelements, so that the small peptide amino acid microelement chelate is produced. The method is suitable for industrial production, the production cycle is short, the product yield is high, the three wastes cannot be produced in the process of production, and the product has good chemical stability, is rich in nutrition, can be easily digested and absorbed, can resist interference, is nonirritant, has the effect of improving the immunity of body, and is an ideal food nutrition enhancer and feed additive. The invention has a positive and profound significance on promoting the development of feed industry and breeding industry, enhancing the safety of poultry, livestock and aquatic products and protecting the health of human being.