In the forward development process of civil aircraft, traditional configuration management, which primarily focuses on the physical implementation end, often leads to inconsistencies between functions, requirements, design configurations, and physical realizations. This study optimized the principles of configuration item identification by refining the logic, timing, and sequence for identifying different types of configuration items. It proposed a product structure centered on the Logical Identification Number (LIN), which explicitly represents the mapping relationships from functional to physical elements. Additionally, the research established the logic for change propagation and validity calculation. Using an air-conditioning refrigeration system as a case study, the model was validated, demonstrating its advantages for improving the efficiency of change-impact analysis, enhancing compliance verification, and ensuring scenario reproducibility.