Modeling is a core practice in science and is a meaningful way to learn the subject. This article introduces a modeling-based approach that highlights the idea that modeling is an iterative process and integrates the fundamental parts of scientists' work and key suggestions for teaching through modeling. The lesson “The Structure and Function of Kidneys” from a middle school biology course serves as an example of how to conduct the suggested modeling-based approach. By the end of the lesson, almost all students demonstrated a scientific understanding of the structure of nephrons and their functions. On the basis of the implementation of this lesson, we also provide further suggestions for modeling-based teaching.