Purpose: It has been acknowledged in physical education (PE) that knowledge empowers learners to develop a physically active lifestyle In this study, we consider Cognitive Load Theory (CLT) as a valuable extension of the constructivist learning theory to help articulate the role of three pivotal instructional factors, content knowledge, learners, and instructional process, in learning fitness knowledge in PE. Guided by CLT, this study was intended to identify middle school students' cognitive architecture about aerobic and anaerobic concepts and pedagogical factors that might enhance or limit scientific conceptualization. Methods: We employed a mixed-methods approach. A total of 291 students randomly drawn from the 24 schools provided data on conceptual knowledge levels via standardized test and conceptual structures of understanding via semi-structured interviews about the aerobic/anaerobic concepts. Results: Results from integrated quantitative and qualitative analyses reveal the role of task element interactivity as a function of conceptualization in the students' cognitive architecture. The students lack the understanding that aerobic and anaerobic concepts are associated with the concepts of complex metabolic systems that dictate the energy pathways experienced in physical activity. Their understandings are characterized by a tendency of overly simplifying the complex conceptions for convenient schema activation. The simplified conception is likely to prohibit their understanding from becoming consistent with the science. The findings suggest that teachers should anticipate lack of understanding of knowledge connectivity when teaching fitness concepts and establish the task element interactivity with enhanced clarity to facilitate knowledge learning. Conclusion: Consistent with the constructivist learning theory, the findings inform us that teaching complex fitness concepts require the teacher to connect prior knowledge as a prerequisite to activate relevant cognitive architecture and actively build connections between the prior knowledge and the to-be learned concepts. PE curriculum designers and teachers should anticipate the complex challenges in teaching the aerobic and anaerobic concepts because of their connections to other concepts associated with human energy systems such as intensity and oxygen supply.