The purpose of this study is to investigate how students understand thermodynamic concepts such as temperature, heat and energy, and how they can enhance understanding of these concepts more easily via computer models. Students often show difficulties imagining matter molecules, temperature, heat and heat energy, some of the subjects studied at high schools in most of developed countries.Semi-structured interviews and writ-ten exams were used to explore students‟ ideas and their mental models. In addition, computers and computer applications are used for this purpose. With 6th grade students, computer models are compared with the traditional educational methods currently dominant in Turkey. They are considered to possess some level of developed concepts of temperature, heat, energy, and matter structure because they have already taken some fundamental courses on these topics. The implications and recommendations for pedagogy are discussed in the conclusion section of this paper.