We evaluated the effect of prolonged summer fishing moratorium on the conservation of fishery resources in Bohai Sea from three perspectives (individual, population, and community) by analyzing the dominant species of nekton, the individual mean body weight, and fisheries resources index of nekton and some main fishery populations or biological categories. Data was collected during trawl surveys in August 2012–2016 and 2017–2021, representing the former and prolonged summer fishing moratorium, respectively. The results showed that the individual mean body weight of nekton in the former fishing moratorium was higher than that in prolonged summer fishing moratorium (4.35 g/ind and 3.77 g/ind, respectively). The individual mean body weight of nekton in the prolonged fishing moratorium decreased, mainly as a result of the annual average density of the populations increasing compared to their annual average resource density, indicating that both the number of complementary populations and the fertility of the parents increased significantly. The dominant species of nekton in the early stage of the prolonged fishing moratorium were Engraulis. japonicus, Oratosquilla oratoria, and Setipinna taty, similar to those in the former fishing moratorium. However, several new dominant species appeared in the later stage of the prolonged fishing moratorium, with a low occurrence frequency and a high annual variation. In general, the dominant species composition of nekton fluctuated greatly throughout the whole fishing moratorium. Meanwhile, body size and the trophic level of dominant species in the prolonged fishing moratorium showed an increasing trend. The annual biomass of nekton, pelagic fish, demersal fish, and crustaceans in the prolonged fishing moratorium were generally higher than those in the former fishing moratorium, especially in the first year. However, the biomass of all of the above biological categories in certain years in the prolonged fishing moratorium were lower than those in the corresponding years of the former fishing moratorium. The annual average biomass of the above biological categories in the prolonged fishing moratorium increased by 186.38%, 178.26%, 357.63%, and 132.89%, respectively. The annual biomass ratio of the bottom to middle and upper organisms in the prolonged fishing moratorium was larger than that in the former fishing moratorium, with an interannual increasing trend. The biomass of higher trophic level organisms remained low in the former fishing moratorium but increased sharply in the prolonged fishing moratorium, showing an increasing trend, with an average annual increase of 493.67% compared with that in the former fishing moratorium. In conclusion, the biomass of both lower and higher organisms in the ecosystem of Bohai Sea in the prolonged fishing moratorium was found to increase significantly, consolidating the energy foundation of the ecosystem, optimizing the community structure of fishery resources, and gradually stabilizing the succession of the ecosystem. These findings indicate that the input control measures of the prolonged fishing moratorium had a beneficial ecological effect in the Bohai Sea.