Most students cannot understand the concepts of science concepts. The abstract concepts that require visualization help students to promote to the understanding about the concept. The aim of this study was to develop Virtual Microscopic Simulation (VMS) in terms of encouraging conceptual change and to promote its effectiveness connected to students' understanding of the microscopic material of heat transfer. The sample consisted of 80 students' whose age ranging from 19 to 21 years old. The VMS related to heat transfer was evaluated through a pre-, post-, and retention tests. The tests scores were analyzed using both qualitative and quantitative methods. The findings suggested that the VMS allows students' to achieve the better understanding of their students' understanding and their significance for the effectiveness of students' understandings.