A simple atom-replacement approach is proposed for estimating the individual contributions of each intermolecular hydrogen bond (HB) in multiple hydrogen-bonded systems. The approach is validated by calculations on the homodimer of formylformamide and then applied to nucleic acid base pairs (adenine-thymine and guanine-cytosine) and some quadruply hydrogen-bonded dimers. With the help of this method, it is easy to distinguish the relative strength of each HB, and identify the main factors contributing to the total binding energies of multiple HBs.