Engineering design process has been recognized as one of the crucial parts of science, technology, engineering, and mathematics (STEM) education. However, when focusing on engineering design process, STEM education at the Kindergarten-12 level often neglects the role of modeling in engineering design process. The characteristic of rapid prototyping of 3D printing technology could be utilized in supporting modeling during engineering design process. This study aims to explore the effectiveness of application of 3D printing technology to STEM project-based learning activities in developing students’ understanding regarding engineering design process, particularly their understanding of modeling. This study employed a quasi-experimental pretest-posttest non-equivalent control group design. A series of knowledge structure analyses showed that in terms of knowledge structures for modeling in engineering design process, the experimental group explained better than the control group in terms of information processing strategies after the teaching experiment.