Natural phenomena and scientific issues are intrinsically interdisciplinary. Students need to study a variety of academic disciplines in the natural sciences to explain a phenomenon or its related problems. Our goal in the current study was to examine the epistemological foundation of students’ interdisciplinary understanding of carbon cycling using the supervised latent Dirichlet allocation model. The 454 students in this study were from a public high school and a public research university in Texas. The students’ interdisciplinary understanding was shown in each of the constructed response items. In the relationship between the proportion of interdisciplinarity in students’ answers to the constructed response items and students’ scores on interdisciplinary understanding, all integrations of disciplines were statistically significant in explaining students’ interdisciplinary understanding. Moreover, one particular integration set had advantages for obtaining a high score. We found that science coursework contributed to students’ interdisciplinary understanding in different ways, and this interdisciplinary understanding was influenced by the number and type of science courses taken. Characterizing interdisciplinarity based on the clusters of science disciplines provided insights into how students synthesize their knowledge. The significance of this study lies in its potential impact on diverse curricular and instructional approaches in interdisciplinary science education.