A study was conducted in 2000 to evaluate impacts of an aquatic environment protection oriented (AEPO) fishery on the structure of food web in Lake Qiandaohu. The AEPO fishery was based on the stocking of silver and bighead carps and the removal of predatory fish and was designed to improve our understanding of ecosystem dynamics to prevent the recurrence of cyanobacterial bloom occurring in 1998 and 1999 and to improve water quality in the Lake Qiandaohu. We constructed Ecopath models of the lake ecosystem for 1999 and 2000, respectively, to compare and analyze quantitatively the changes of the food web structure before and after the implementation of AEPO fishery in the lake. The results showed that AEPO fishery resulted in a reduction of ice fish and common carp biomass and an increase of Culters (esp., Culter mongolicus), Xenocypris and Sinibrama biomass, etc., reducing the niche overlap of both preys and predators in the ecosystem. In addition, The AEPO fishery enhanced the bottom-up effects of bighead carp and silver carp on predatory fish such as Elopichthys and Culters, reduced the suppressing effects of Elopichthys on Culters, of Culters on shrimp, ice fish and common carp, and of ice fish on zooplankton, and enhanced the inhibitory impacts of bighead carp on ice fish, Sinibrama and common carp. These effects of AEPO fishery, making the food web structure optimal such as increasing detritivorous fish like Xenocypris, can result in the enhancement of nutrient recycling and reutilization, eventually leading to the enhancement of purification capability of the lake ecosystem.