The invention belongs to the technical field of fertilizer production and relates to biological semi-organic fertilizer containing amino acid and a making method thereof. Urea, monoammonium phosphate, potassium sulphate and bentonite are matched reasonably, amino acid mother liquor granules are adopted to form granulation master batch, aminated humic acid, medium trace element compositions, decomposed coal and amino acid mother liquor are blended to form a coating sizing agent used for primary coating of the granulation master batch, then a dusting powder agent is formed by microorganism bacterial liquid and calcium carbonate powder, a coating agent is formed by white oil, molasses and a mixture, and secondary coating is conducted in a coating machine to generate the biological semi-organic fertilizer containing amino acid. The biological semi-organic fertilizer containing amino acid has the efficiency of humic acid, amino acid, biological agents and the like and also has a slow-releasing function, effective constituents can be released slowly and orderly, fertilizer efficiency is remarkable, and production organization is facilitated.