Many researchers have suggested that incorporating history and philosophy of science in the science curriculum can be helpful for students’ understanding of scientific concepts and effective for developing their scientific thinking. Recently, in this context, there have been studies on historical controversies which show that history of science promotes debate and controversy and thus sustains students’ effort to understand what is being taught. However, existing studies have only searched and selected what the historical controversial issues exist and have not dealt with more practical issues such as how to use them in the classroom. In this study, for finding guide to teach controversial issues in history of science, we analyzed controversial issues related to the structure of the atom to understand their structure by using the ‘framework of knowledge and belief’. As a result, it was confirmed that the structures of the historical controversies consisted of various forms from the conceptual level to the belief level. Finally, the implications related to the use of the result of this study in the classroom, and to science education research were discussed.