To study the changes in food web structure in the process of ecological restoration of Yidian Lake, this study was conducted in the experimental area of the Shihoudian lake by planting submerged plants to build artificial fish nests. Based on the investigation data of fish resources and ecological environment of Shihoudian Lake in 2019, the structure and energy flow characteristics of the two regional ecosystems were compared and analyzed using Ecopath with the Ecosim software and ecosystem energy channel model. The results showed that the trophic level of the same fish species in the experimental area was slightly lower than that in the control area. The niche of the same species in the ecological restoration area was lower than that in the control area. Meanwhile, there were more consumers in the former food chain, such as catfish (Siluriformes), mandarin fish (Siniperca chuatsi), Wuchang bream (Megalobrama amblycephala), and grass carp (Ctenopharyngodon idellus). Complex structure suggest a stable food web. In addition, the energy conversion efficiency among the trophic levels in the experimental areawas was higher than that in the control area. The total energy conversion efficiency (2.5%) in the experimental area was higher than that in the control area (1.7%); the connection coefficient (0.22) in the experimental area was slightly lower than that in the control area (0.27); the system omnivorous index (0.15) was higher than that in the control area (0.14); and the Finn’s cycle index and average path length (0.61 and 2.08, respectively) in the experimental area were lower than those in the control area (1.73 and 2.20, respectively). The overall characteristics of the two regional ecosystems showed that the structure of the food web in the experimental area was more complex, the energy transfer efficiency was improved, and the ecosystem was more perfect. However, the length of nutrient flow through the food chain in the experimental area was shortened, and the proportion of material recycling was decreased. At the same time, the production was greater than the respiration in the experimental area. Thus, further implementation of restoration measures for fish resources would be conducive to development of the ecosystem in the experimental area.