The focus on STEM has centered on knowledge use across multiple disciplines. However, there currently exists limited understanding of the relationship between the cognitive practices utilized across these disciplines as a function of performance on standardized assessments. Focusing on science and mathematics, we investigated the direct and indirect relationships between science and mathematics reasoning practices. The TIMSS 2011 cognitive practices were adopted to establish a hypothesized model representing these relationships. We employed the generalized DINA (deterministic inputs, noisy "and" gate), confirmatory factor analysis (CFA), and structural equation modeling (SEM) to 2287 fourth-graders' responses to standardized mathematics and science assessments. The findings show positive relationships among science reasoning, mathematics reasoning, and mathematics applying. However, we also found a significant indirect effect from science reasoning to mathematics reasoning through mathematics applying. This result calls for a need to shift the focus of interdisciplinary efforts to emphasize cognitive practices that students use in learning mathematics and science as suggested in the Next Generation Science Standards and the Common Core State Standards for Mathematics.