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The primary goal of the current study is to examine the epistemological foundation of how students’ interdisciplinary understanding of carbon cycling is shown using the supervised latent Dirichlet allocation model. The students’ interdisciplinary understanding was displayed in a variety of scientific disciplinary combinations. In the relationship between the proportion of students’ interdisciplinarity understandings and their scores, all integrations of disciplines were statistically significant in explaining students’ interdisciplinary understanding. Moreover, a specific integration set had more advantages in obtaining a higher score. Characterizing interdisciplinarity based on the clusters of science disciplines provided insights into how students synthesize their knowledge in the cognitive mechanisms. The findings will have a potential impact on diverse curricular and instructional approaches in interdisciplinary science learning.