Understanding the general ideas and methods of detecting molecular structures is essential in high school chemistry. However, there is a need for more practical activities in teaching. A hands-on activity was designed in this study, which uses flexible foam balls and long sticks such as knitting needles to imitate how scientists construct the 3D molecular structure model. The activities mainly included retrieving the crystallographic data from the crystal database; converting the microscopic molecular coordinates to macroscopic coordinates; building the spatial position model according to coordinates; and inferring atomic bonds according to structural information and bond length. The process allowed students to get a magnified, complete 3D physical molecular structure model. The activity aimed to develop students' understanding of the molecular stereo structure and the process of model construction, which can also make students realize the unknown nature of research objects and the construction nature of scientific understanding.