This study explored the educational value of using GeoGebra in lessons on crystal structure learning. To this end, a four-session course utilizing GeoGebra was conducted for 50 students taking Chemistry II at M Girls’ High School in Jeollanam-do. The understanding of crystal structure concepts was assessed through pre- and post-tests, and changes were examined using paired sample t-test. Course satisfaction was measured in the post-test using a 5-point Likert scale and open-ended questions. The results are as follows: First, the students showed a significant increase in understanding all three crystal structures (p<0.001), particularly noted by the decrease in non-responding students in the post-test, indicating meaningful changes for students with lower learning levels. Second, the course satisfaction, as measured by the Likert scale, was high, ranging between 4.46 and 4.62. The students’ responses highlighted that the use of GeoGebra not only aided in conceptual learning but also facilitated scientific inquiry. This study suggests the value of tools like GeoGebra in science education, particularly in utilizing sub-microscopic like the particle model.