Silver and bighead carp (Hypophthalmichthys molitrix and Aristichthys nobilis) are typical filter-feeding fish that are important species for the implementation of water purification fishery, and scientific stocking based on the ecological capacity of the proliferating species can ensure the implementation effect of water purification fishery. To ensure the implementation of water purification fishery in the Taihu Lake, we constructed an Ecopath model comprising 16 functional groups. This model was based on the survey data of fishery resources and the ecological environment of the Taihu Lake in 2017–2018. Relevant data was collected using Ecopath with Ecosim 6.6 to estimate the ecological capacity of silver and bighead carp in the Taihu Lake and to investigate the effects of changes in silver and bighead carp biomass on the overall characteristics of the Taihu Lake ecosystem. The results showed that the current biomass of the silver and bighead carp was 10.21 t/km² , which increased 5.054 times to reach an ecological capacity of 51.6 t/km² . It is showed that there is still great potential for the growth of the silver and bighead carp. Total primary production/total respiration decreased from 2.548 to 2.23 (change of 0.318). Connectance index, system omnivory index, Finn’s cycling index, and Finn’s mean path length exhibited fewer changes. Silver and bighead carp exert less impact on the ecosystem structure when they reach the ecological capacity, but nevertheless help the ecosystem to mature. Further analysis shows that when Coilia nasus is controlled at 9.49 t/km² , the biomass capacity of the silver and bighead carp could increase to 206.4 t/km² , and when the silver and bighead carp reach their ecological capacity, the ecosystem will become more stable.