Polypeptides have inherent secondary structures, such as alpha-helix,) beta-sheet, and random coil structures, depending on their amino acid sequence. beta-Cyclodextrins (CDs) as ligands of molecular recognition sites were introduced into poly(Llysine) (PLL), which undergoes a structural transition in response to a pH change. CD-introduced PLL (CD-PLL) hydrogels with dynamic molecular recognition sites for bisphenol A (BPA) were strategically designed by molecular imprinting, where BPA was used as a template molecule with a minute amount of cross-linkers. The resulting BPA-imprinted CD-PLL hydrogels with a random coil structure underwent a change in volume in response to the target BPA because the ligand CDs formed a complex with BPA. Additionally, a change in pH induced a structural transition of the CD-PLL chains from the random coil to an a-helix, followed by a conformational change of the molecular recognition sites within the BPA-imprinted CD-PLL hydrogels. As a result, BPA adsorption into the BPA-imprinted CD-PLL hydrogels strongly depended on pH. The molecular recognition ability of the BPA-imprinted CD-PLL hydrogels was controlled by the helix coil transition of the PLL chains. BPA, as a model drug, was loaded within the CD-PLL hydrogel networks by molecular imprinting, and the BPA template was not extracted from the hydrogel networks. The drug release from the drug-loaded CD-PLL hydrogel was regulated by the pH-responsive structural transition of the PLL chains, which could control the stability of the inclusion complex between the drugs and CD ligands. The fascinating properties of the BPA-imprinted CD-PLL hydrogels with dynamic molecular recognition sites suggest that they exhibit potential as suitable drug carriers inspired from the allosteric effects of proteins.