Predation and competition are the main factors regulating population dynamic of freshwater organisms and also the most important structuring forces in freshwater ecosystems. Lake Qiandao is a large deep reservoir where pelagic community is dominated by silver carp Hypophthalmichthys molitrix and bighead carp Aristichthys nobilis. In order to understand the effects of biological factors affecting zooplankton community structure in the upper, middle, and lower reaches of Lake Qiandao, a two-year study was conducted monthly from 2009 to 2010. Pearson correlation analysis and stepwise multiple regression were applied to identify the major biological factors influencing zooplankton community variations. Comparing the data to the previous studies, the present study revealed that the biomass of silver carp and bighead carp in 1999 was one fifth of the average in 2004 and in the period from 2007 to 2010, and the biomass of rotifer and copepod almost kept constant, while Daphnia hyaline biomass decreased substantially which was caused by the decrease of phytoplankton biomass. Hence, we suggest the bighead carp might affect the zooplankton community structure significantly in Lake Qiandao.