Water quality oriented fishery is one of the measures to control ecological disasters such as water bloom outbreak in China, but the subsequent results are quite uncertain. In Xin'anjiang Reservoir (Qiandao Lake) of Zhejiang Province, the implementation of water quality oriented fishery has brought certain positive effects on the water quality improvement and fishery production. However, the structural effects of such anthropogenic interventions on ecosystem self-organization has remained a significant challenge. In this study, we collected the ecological and fishery resources data of Qiandao Lake from 2008 to 2010 to construct the Ecopath model, dividing the ecosystem of 2010 into 17 functional groups. The ecosystem structure and functional status of Qiandao Lake in 2010 was compared with those in 2004 and 2016 based on our analysis of the Ecopath model, in order to explore the effects of stocking silver and bighead carp. The results showed that the ecosystem of Qiandao Lake in three typical years all mainly consisted of four integrated trophic levels with a typical pyramidal-shape energy flow, and the flow to detritus accounts for a large proportion in the total nutrient flow, thus it can be seen that the energy of trophic levels Ⅰ and Ⅱ was not fully utilized. Except for silver carp and bighead carp, the overall fish stock decreased gradually, while the biomass of phytoplankton and detritus increased simultaneously. The primary production and scale of the system improved to some extent, but the total energy transfer efficiency of the system was not high compared to other reservoirs. In terms of some parameters closely related to system maturity, resilience and stability, the total primary production/total respiration (TPP/TR) increased, and Finn's cycling index and Finn's mean path length decreased gradually, accompanied with relatively low connectance index and system omnivory index in all three typical years (CI=0.223, 0.219, 0.263, respectively; SOI=0.087, 0.102, 0.131, respectively). The results indicated that long term stocking of silver carp and bighead carp had resulted in a significant change in the food web of Qiandao Lake, and the overall decline of fish resources might lead to over nutrition in the lake. The ecosystem trophic interactions were not complex enough, and the maturity and stability were reduced. As a fresh water body developed from the reservoir, the relationship between food webs in Qiandao Lake is relatively simple. Therefore, it is necessary to carry out restoration work to avoid too much human interference, and a more systematic restoration measure based on ecological principles is needed in the future.