Salt marshes are one of the three blue carbon ecosystems recognized by the Intergovernmental Panel on Climate Change (IPCC). However, coastal salt marshes in China are facing the risk of degradation. To reveal the status of the salt marsh wetland ecosystem in Liaohe Estuary, an Ecopath model composed of 14 functional groups was constructed based on the 2019 ecological survey data. A comprehensive analysis of the system’s food web structure, energy flow processes, and overall ecosystem characteristics was conducted. The results show that the energy flow in the Liaohe Estuary salt marsh wetland ecosystem is mainly distributed in three integrated trophic levels. The utilization rates of trophic levels II and III are low, easily causing blockages in the lower trophic levels of the ecosystem’s energy flow. The total system throughput of the Liaohe Estuary salt marsh wetland ecosystem is 49,099.039 t·km²·a−1;. The system connectivity index and the system omnivory index are 0.207 and 0.109, respectively. Compared with other wetland systems, the ecosystem has a larger scale, but the overall ecosystem characteristic index reveals lower stability and complexity of the Liaohe Estuary salt marsh wetland system.