This research aimed to explore the upper-secondary school chemistry teachers' and students' conceptual structures of atomic structure by using multidimensional scaling. Atomic structure is considered to be one of the most difficult concepts in upper-secondary school chemistry course so that the conceptual structure regarding atomic structure held by the learners is necessary to be examined. Based on a questionnaire survey for upper-secondary school chemistry teachers and university chemistry professors, 40 concepts were selected as a useful concept pool of atomic structure. Then, the conceptual structures and the specific classifications of concepts from 168 upper-secondary school chemistry teachers and 336 tenth-grade students were investigated by multidimensional scaling and hierarchical cluster analysis. The results showed that the 3-D solutions were appropriate for the conceptual structures of teachers and students, respectively. Next, the conceptual structure of teachers utilized as an evaluation criterion was more scientific than that of students. The conceptual structure of students with high academic achievement was more scientific than that of the low achievers. Multidimensional scaling utilized to explore students' conceptual structure of scientific concepts can provide a new and benefic form of evidence to understand the concept learning outcome of students.