The goal of this study was to identify and understand the mental models developed by 67 high school biology students as they learn about the human body as a complex system. Using concept maps, it sought to find an external way of representing how students organize their ideas about the human body system in their minds. We conducted a qualitative analysis of four concept maps created by each student throughout the 3-year learning process, which allowed us to identify that student's systems thinking skills and the development of those skills over time. The improvement trajectories of the students were defined according to three central characteristics of complex systems: (a) hierarchy, (b) homeostasis and (c) dynamism. A comparative analysis of all of our students' individual trajectories together revealed four typical learning patterns, each of which reflects a different form of development for systems thinking: "from the structure to the process level", "from macro to micro level", "from the cellular level to the organism level," and "development in complexity of homeostasis mechanisms". Despite their differences, each of these models developed over time from simpler structures, which evolved as they connected with more complex system aspects, and each indicates advancement in the student's systems thinking.