Abstract: The accurate calculation of the carbon emission indicator on the user side is the key to guiding the usage of low-carbon energy for users. However, the current carbon trajectory tracking methods for integrated energy systems only consider steady states, which cannot accurately calculate the carbon emission indicators of the natural gas and thermal system with significant load variation and long dynamic processes. Therefore, based on the superposition principle, the energy flow tracking and carbon entropy analysis of dynamic natural gas and thermal systems are carried out. Firstly, the dynamic energy flow model based on the superposition characteristics of the natural gas and thermal systems is established. Then, the energy flow is tracked by taking the line pack in the natural gas network and the time delay in the thermal network into consideration, and the source-load energy flow relationship within the system is defined. Secondly, based on the carbon entropy theory, the dynamic carbon entropy analysis methods of natural gas and thermal systems are proposed to clarify the source-load carbon emission relationships, and refined carbon emission indicators on the user side are formed. Finally, an integrated energy system in Jilin Province, China is taken as a case to verify the effectiveness of the model in dynamic energy flow analysis and carbon entropy analysis. The necessity of dynamic carbon trajectory tracking is also verified by comparing the model with the steady-state carbon trajectory tracking method.