The use of molecular models in chemistry and biochemistry classes is very effective in helping students understand covalent bonds and the chemical structure of molecules. However, conventional molecular models cannot represent intermolecular interactions such as hydrogen bonds and electrostatic interactions. Herein, we describe 3D printed molecular models of nucleobases with the S and N poles of neodymium magnets placed as the donor and acceptor atoms of hydrogen bonds, respectively. The molecular models, called BasePairPuzzle, allow the user to experience manually how molecular recognition occurs when molecules attract or repel each other. This helps to understand the concept of hydrogen bonding and electrostatic interactions. By playing with two or more molecular parts, by attaching and detaching them, users can understand and realize various biological phenomena at the molecular level, such as why DNA forms complementary A-T and G-C base pairs to store genetic information, how DNA mutations can occur, and how nucleic acids can form various noncomplementary base pairs to have complex structures and functions other than storing and transmitting genetic information. In addition, for professional research scientists, the molecular models can support the discovery of new molecular design ideas in drug discovery and nanotechnology.