This study investigates how elementary students were able to construct a human respiratory system model and, in particular, how the process of reasoning contributed to their model through the use of analogy model activities. For this study, modeling activities that included the use of analogy models were designed and implemented. Over 4 class periods in which analogy model activities were used, 18 fifth- and sixth-grade elementary students were asked to construct a model of the human respiratory system, showing the system's structure, function, and mechanism. By engaging in activity with a syringe analogy model, several elementary students developed their model from a function-centered model to a mechanism-centered model, whereas others elaborated their model from a mechanism-centered model to an elaborated mechanism-centered model via activity with a balloon-lung analogy model. During model construction, the analogy model activities played a facilitating role in helping students to construct the invisible mechanisms, based on the model-based reasoning, and to elaborate their model by considering the sub-structures' movement within the system. This study provides additional discussions of the ways in which model activities can support the students' reasoning in the modeling process.