A synthesis method of alanyl-glutamine includes the steps of: The N-terminal protected alanine reacts with triphenylphosphine and hexachloroethane in organic solvent to form active ester, the active ester reacts with glutamine in a solution mixture containing organic solvent and aqueous solution of inorganic base, the resultant mixture is acidified with inorganic acid, and then the N-terminal protecting group is removed. In this method, the raw materials are cheap, the synthesis technique is simple, no disposals of separation and purification are needed, the product is easy to be separated and purified, the toxicities of all the reagents used in the course of production are minimal, it is advantageous to environment protection.