The invention discloses a synthesis method of a cyclic dipeptide. A cyclic dipeptide sequence contains L-asparagine or L-glutamine. The method comprises the following steps: by taking 2-Chlorotrityl Chloride Resin as a carrier, carrying out solid-phase synthesis to obtain a straight-chain dipeptide fragment H-Glu-AA-OH or H-Asp-AAOH, wherein AA is other alpha-amino acids except asparagine, glutamine, glutamic acid, aspartic acid and cysteine; then carrying out a methyl esterification reaction to obtain straight-chain dimethyl ester protected dipeptide H-Glu (OMe) -AA-OMe or H-Asp (OMe)- AA-OMe; then carrying out water-phase alkaline cyclization to obtain cyclic dipeptide Cyclo[ Glu (OMe)- AA] or Cyclo[ Asp (OMe)- AA] protected by side chain carboxyl methyl ester; and finally, carrying outammonolysis to obtain the cyclic dipeptide containing glutamine or asparagine. The method is simple in synthesis process and safe to operate, incomplete cyclization caused by steric hindrance of aminoacid side chain protecting groups in the cyclization process is effectively avoided, few byproducts are produced, purification is easy, and cyclic dipeptide containing Gln and Asn can be synthesizedin batches.