Lysine acetylation is a widespread protein post-translational modification (PTM) that plays a central role in diverse physiological processes. The study on the scope and pattern of lysine acetylation is an important subject in the proteomic research. However, identification of lysine acetylation from biological sources is a great challenge due to the low abundance in the massive background of unmodified proteins and the dynamic fashion of the modifications. In this research, a novel molecularly imprinted polymer (MIP) with high affinity for peptides containing acetylated lysine (Kac) has been synthesized by the combination of an epitope and surface-confined imprinting strategy. A dipeptide: KacA, containing acetylated lysine and alanine residues, was used as the template and immobilized on the sacrificial silica support. After hierarchical imprinting and removal of silica, the surface-confined cavities were created on the resulting KacA-MIP material. The equilibrium binding and HPLC experiments demonstrated that the KacA-MIP has good selectivity and epitope affinity. It can differentiate Lys-acetylated peptides (Kac-peptides) from their native structures and has higher affinity for Kac-peptides with different sequences. The selectivity of the MIP was also proved by its ability in the extraction of Kac-peptides from spiked histone digest and by its enrichment performance in the whole cell lysates. The study developed a method of MIP preparation with affinity for PTM peptide based on recognition of peptide side chains. It also indicated that the MIP has potential to be used as an antibody mimic in the PTM analysis.