Introducing an internal circulation loop boosts aircraft Thermal Management System (TMS) heat sink efficiency. However, it creates complex dynamics with flow-dependent response delays. TMS couples thermodynamic and fluid dynamic processes, featuring numerous interconnected nodes that exhibit high heterogeneity and complexity. Conventional modeling fails to capture these dynamics or analyze delay causes, hindering control design. This paper proposes a hierarchical (hydraulic-thermal) graph-based modeling method for internal loop TMS dynamics. It reveals delay mechanisms and quantifies delay zones across flow states. The results show that the fundamental cause of the delay effect is that the internal circulation alters the topological structure of system dynamics and adds positive feedback terms, and the larger the flow rate of the internal circulation, the slower the system response speed.