One of the key goals of science education is to enable students to acquire scientific concepts. Most science concepts are learned through teachers in class. Therefore, this study analyzes conceptual structure that teachers use to teach students and the conceptual structure that students develop as they learn new concepts. Specifically, we examined the differences between the conceptual frameworks used by teachers to teach students and the networks of concepts that students actually acquire, focusing on the topic of photosynthesis in middle school. Within the domain of photosynthesis, we categorized concepts into the photosynthesis reactants, photosynthesis products, environmental factors. This study revealed that the types of concepts used by teachers in class and those acquired by students are similar, but the network structures differ. Teachers do not clearly distinguish and explain subtopics, and students also do not distinguish subtopics to acquired concepts. Teachers focus on explaining concepts, and students’ conceptual networks are influenced by subsequent learning as well. Based on these findings, it is crucial for teachers to understand the conceptual structures that students develop and to clearly articulate sub-concepts to guide their learning effectively. Furthermore, future research should explore whether there are variations in acquired conceptual networks based on characteristics of the learners.