The complexation of β-lactam antibiotics, amoxicillin (AMPC), ampicillin (ABPC) and benzylpenicillin (PCG), with 2-hydroxypropyl-β-cyclodextrin (HPCD) was studied at various pH values using microcalorimetry, 1H NMR spectroscopy, and molecular dynamic simulation. In the strong acid solution, two different types of inclusion complex with a 1:1 stoichiometry, Complex I with a phenyl ring of β-lactam antibiotics penetrated into the cavity of HPCD and Complex II with a penam included in the cavity, were formed by hydrophobic interaction, and Complex II was more stable than Complex I. In aqueous solution at pH≥4.5, only Complex I was formed, where the penam of PCG was more deeply penetrated into the cavity to keep it stable than those of AMPC and ABPC. The charged carboxyl-group on the penam was less affinity to form Complex II.