Chemical synthesis of proteins bearing base‐labile post‐translational modifications (PTMs) is a challenging task. For instance, O‐acetylation and S‐palmitoylation PTMs cannot survive Fmoc removal conditions during Fmoc‐solid phase peptide synthesis (SPPS). In this work, we developed a new Boc‐SPPS‐based strategy for the synthesis of peptide C‐terminal salicylaldehyde (SAL) esters, which are the key reaction partner in Ser/Thr ligation and Cys/Pen ligation. The strategy utilized the semicarbazone‐modified aminomethyl (AM) resin, which could support the Boc‐SPPS and release the peptide SAL ester upon treatment with TFA/H2O and pyruvic acid. The non‐oxidative aldehyde regeneration was fully compatible with all the canonical amino acids. Armed with this strategy, we finished the syntheses of the O‐acetylated protein histone H3(S10ac, T22ac) and the hydrophobic S‐palmitoylated peptide derived from caveolin‐1. A Boc‐SPPS based method towards the synthesis of peptide C‐terminal salicylaldehyde esters compatible with all canonical amino acids was developed. The method could facilitate the synthesis of proteins bearing base‐labile post‐translational modifications, e.g., O‐acetylation and S‐palmitoylation.