Based on the ecological survey data in 2022, the Ecopath models of the Mulan River Estuary and its upstream and downstream control areas (river area and bay area) were constructed, and the trophic structures, energy flow characteristics, and overall system characteristics of the three ecosystems were comparatively analyzed. The results indicate that the trophic structures of the Mulan River Estuary, river, and bay ecosystems are all pyramid-shaped, and the structural complexity from low to high is river, estuary, and bay, successively; the energy flows in the three ecosystems are mainly concentrated in trophic levels Ⅰ-Ⅲ, with energy flow proportions all above 99%; the total energy transfer efficiency (TE) of the estuary ecosystem is relatively low (0.9%); benthos and phytoplankton are the key trophic communities affecting the estuary ecosystem; the ratio of primary production to respiration (3.33), Finn’s cycling index (0.085), and Finn’s mean path length (2.683) of the Mulan River Estuary are between those of the river and the bay, while the connectance index (0.32) and system omnivory index (0.051) are the smallest, indicating that the estuary ecosystem is still in an immature and unstable stage; the increases in NO₃-N and CODMn may affect the maturity and complexity of the ecosystems; it is recommended to improve water quality by implementing reasonable and effective water environment treatment measures and to improve the maturity and stability of the estuary ecosystem by moderately increasing the stock enhancement and release quantity and species of herbivorous and carnivorous fishes.