Abstract: Ecopath with Ecosim (EwE) model is commonly used to quantitatively study the food web structure and energy flow characteristics in the aquatic ecosystem. The principles and progress of Ecopath, Ecosim, Ecospace, and Ecotracer modules of EwE model and its application in different types of aquatic ecosystems were summarized. The results indicated that Ecopath could be used to estimate the maturity of the ocean and freshwater ecosystems, to determine key species and ecological capacity, and to clarify the important contribution of phytoplankton production (P) to total system throughput (TST) in the aquatic ecosystem. Ecosim was used to reveal the impact mechanisms of human activities (e.g. keystone species catching, port construction) on ecosystem structure and function on a time scale. Ecospace was used to clarify spatial variability of fishing activity and ecosystem structure under external factor effects (e.g. offshore platform construction, power plant operation, and volcanic eruption). Ecotracer was used to trace the immigration progress of isotopes, heavy metal, new pollutant, and other matters in the food web. Combined with Ecopath, the nutrient structure and energy flow of Changtan Reservoir were analyzed. The results showed that the trophic level was in the range of 1.000-3.093, indicating a simple food web structure. The total primary production/total respiration (TPP/TR) value was 2.445, indicating Changtan Reservoir was a relatively mature ecosystem, and it had a low energy transfer efficiency. In the future, studies on the impacts of climate change and human activities on the structural succession of aquatic ecosystems, and the enrichment characteristics of new pollutants in the food web should be strengthened to provide a scientific basis for the assessment of aquatic ecosystem health and the adjustment of fishery economic development policies.