Imidazole-promoted ligation of peptide phenyl esters was recently found to be a complementary method for protein chemical synthesis. Theoretical calculations have been carried out to understand the detailed mechanism of this particular ligation process. It is found that both the reaction of the phenyl ester with imidazole and the reaction of the acyl imidazole intermediate with cysteine proceed through an addition-elimination mechanism. The cleavage of the CO bond in the reaction between the phenyl ester and imidazole is the rate-limiting step of the overall ligation process. Interestingly, although the imidazole-promoted phenyl ester ligation has a higher free energy barrier than the conventional thiophenol-promoted native chemical ligation for a sterically less hindered C-terminal amino acid (e.g. gylcine), for a sterically hindered C-terminal amino acid (e.g. proline) the imidazole-promoted phenyl ester ligation is calculated to be more favorable than the conventional thiophenol-promoted native chemical ligation.