The main goal of STEM education is to provide students with knowledge and skills in science, technology, mathematics, and engineering through interdisciplinary approaches. However, perspective on the nature of STEM approaches and how it should be implemented in the classrooms without losing discipline integrity are still not uncovered and stay as important challenges for both educators and researchers. In this paper, we introduce a theoretical framework that can shed light on how to engage students effectively in STEM education by providing mathematical modeling as a tool for integrating different disciplines. Thus, this framework is for designing, implementing, and evaluating mathematical modeling thinking within an interdisciplinary nature. Furthermore, we provide an example of the interdisciplinary mathematical modeling task with hypothetical student engagement in the process and analyzed the student's thinking with our framework. Although the focus of this paper is mainly about integrating mathematics and science, we believe that our framework can be applied to all STEM disciplines. We conclude that interdisciplinary mathematical modeling framework might be an important tool to overcome some of the challenges that stressed in the literature since it increases the transfer capacity of STEM-focused knowledge and skills to real-world scenarios by presenting problem situations in a real-world context.