Abstract: The impacts of stocked silver carpHypophthalmichthysmolitrixand bighead carpAristichthysnobilison phytoplankton community structure in the Three Kingdoms City, Taihu Lake by comparison of the differences of phytoplankton community structure between inside and outside fencing from August to November, 2016, and the water quality in the Three Kingdoms City was analyzed by comprehensive nutritional status index and biodiversity index to evaluate the relationship between environmental factors and phytoplankton community. A total of 90 species in 44 genera, 6 phyla was found,with dominant species cyanobacteria. Analysis of variance indicated that there was no significant difference in species composition and diversity within and outside fencing area (P>0.05). GenusMicrocystishad more density and biomass, significantly lower inside the fence than those outside the fence (P<0.05). Comprehensive evaluation revealed that the water quality in the Three Kingdoms City was within the middle and heavy pollution eutrophic water bodies, better inside the fence than outside. Correlation analysis indicated that phytoplankton density, biomass and cyanobacteria density were significantly positively correlated with water temperature (P<0.01), and negatively correlated with dissolved oxygen level (P<0.01). RDA analysis showed that phytoplankton within the fence was closely related to water temperature, dissolved oxygen, pH and CODMn, while the water temperature, dissolved oxygen, pH and transparency showed more effect outside the fence. The findings indicate that the stocking of silver carp and bighead carp is suitable for control algal blooms instead of algal aggregates, and that the releasing pattern of silver carp and bighead carp for control algae is needed further research.