Carbon cycling is a key natural system that requires robust science literacy to understand how and why climate change is occurring. Studies show that students tend to compartmentalize carbon movement within plants and animals and are challenged to make sense of how carbon cycles on a global scale. Studies also show that students hold faulty models of climate change which thwart their reasoning about how and why climate change occurs. Very few studies have examined how to support students in understanding carbon cycling and reasoning about the relationships between carbon cycling and climate change. To support secondary students in making these connections, we developed a modeling‐centered socio‐scientific issue (SSI) based curriculum unit taught by the same teacher across three sections of a secondary biology class. At three time points within the 2‐week unit, 50 students developed, used, evaluated, and revised their own carbon cycling models to use as sense‐making tools for how individual biological processes create a global carbon system and the relationship between carbon cycling and climate change. A small subset of students (n = 16) were also interviewed about their models. We constructed holistic scoring rubrics to document students’ model‐based reasoning associated with each model and then compared rubric scores across time points to examine potential progression of model‐based reasoning over the course of the unit. Results suggest that students’ must hold a robust understanding of causal mechanisms for transfer and transformation of carbon in order to make connections between carbon cycling and climate change. Once their understanding of carbon cycling becomes robust, their reasoning shifts in complexity to understand interrelationships between carbon cycling and climate change. Implications from this study suggest that embedding the practices of modeling within a SSI unit supported secondary students in building robust understanding of carbon cycling and the interrelationship to climate change. © 2017 Wiley Periodicals, Inc. J Res Sci Teach 9999:XX–XX, 2017