This research aims to identify the concepts that elementary school students struggle to understand in their science classes and to overcome these difficulties by utilizing a design thinking model. Specifically, the impact of instructional methods based on the use of 3D models on students' academic achievements has been examined. Additionally, students' opinions on the use of solid 3D models in the classroom were collected. The study adopted a mixed method approach. The sample of the research consists of 3rd grade (N=31) and 4th grade (N=29) students attending an elementary school in the Akçaabat district of Trabzon province. This study used a mixed-method research design. Accordingly, in the "Empathy" phase based on the design thinking model, the concepts in the science course units that elementary school students found difficult to understand were identified through the "Teacher Opinion Form" prepared by the researchers, collecting views from 20 classroom teachers. Subsequently, statistical, and descriptive analyses of the teachers' responses were conducted, determining that the leading concepts students struggled with were "The Structure of the Earth" for the 3rd grade level and "The Structure of the Earth's Crust" for the 4th grade level. In the "Define the Problem" and "Ideation" phases of the Design Thinking Model (DTM) model, the researchers decided which three-dimensional models could be designed for teaching these topics. Initial two-dimensional drawings were made, and designs were developed using 3D pens in the "Prototype Development" phase. The computer-based drawings of the pre-designed models were completed, and prints were obtained from 3D printers. Before using the final models in the lessons, a "Concept Achievement Test" consisting of 10 questions each was administered as a pre-test to the students. One week after the pre-test application, the teaching process using the final models was conducted by the researchers. Three days after the interactive use of the 3D models in the classroom, the post-tests were administered. In the post-test, students were also asked two open-ended questions about their opinions on the use of 3D models in science classes. The research findings indicate that the lessons conducted using the design thinking model and 3D modeling had a significant effect on the students' understanding of science topics. A comparison of pre-test and post-test results revealed a statistically significant improvement favoring the post-test for both 3rd grade (t=-5.005; p<.05) and 4th grade (t=-2.813; p<.05) students. The use of models facilitated the students' learning processes and helped them better understand the concepts at both grade levels. Moreover, by making the lessons more fun and interactive, they increased students' interest in science. The results of the research demonstrate that the design thinking approach and three-dimensional models enhance understanding and comprehension levels in elementary school science classes. These findings can serve as an important resource for educators and policymakers in developing teaching methods that support active learning processes and encourage conceptual understanding. It is also suggested that the applicability of such innovative teaching strategies in other subjects should be explored.