The invention provides a method for stabilizing polypeptide into an alpha spiral secondary structure. The method comprises the following steps: (1) connecting the amino terminals of the polypeptide to non-natural amino acid, then endcapping the polypeptide through acetylation reactions; (2) subjecting the reaction production obtained in the step (1) to sulfydryl-alkene reactions so as to obtain a polypeptide compound whose side chains are modified by thioether; (3) oxidizing the obtained thioether modified polypeptide compound to obtain a R-type or S-type polypeptide compound whose side chains are modified by sulfoxide; (4) separating and purifying the reaction product obtained in the step (3) so as to obtain the R-type polypeptide compound whose side chains are modified by sulfoxide. The method utilizes chiral sulfoxide to modify the side chains of polypeptide so as to stabilize the alpha spiral secondary structure of polypeptide, it has been proved by CD that the effect is very good, and the durability of sulfoxide on polypeptide sequence is good.