Disclosed in the present invention is a method for preparing Exenatide. Serine resin is obtained through a first coupling of serine and resin and successively with amino acids through a second coupling to obtain a peptide resin with a sequence as shown by SEQ ID No. 1; Exenatide resin is obtained through a third coupling of histidine containing a protecting group or salts thereof and the peptide resin with a sequence as shown by SEQ ID No. 1, then it is cracked and purified to obtain purified Exenatide peptide. The method for preparing Exenatide of the present invention inhibits the formation of D-His-Exenatide, and thereby improves the yield and purity of Exenatide.