Branched peptide as an attractive mimic of natural peptide is widely used in structural design of functional or therapeutic peptides, to improve their biological activity, stability, and pharmacokinetic properties. In this protocol, we employ a function group of side-chain benzyl ester as the precursor of hydrazide, which could be conveniently used to assemble a branch peptide by native chemical ligation or direct amidation. This method is convergent and efficient, and facilitates the synthesis and application of branched peptides.