Turbulence is an intrinsic and ubiquitous characteristic of aquatic environments, especially in large shallow lakes which are strongly influenced by wind-driven disturbances. Turbulence could also drive the changes of physico-chemical characteristics and biological communities of the water column, like in zooplankton species. However, the direct physical effects of turbulence on the dynamics and structure of zooplankton communities has not been well understood especially in lake systems. In this study, a 15-day mesocosm experiment was carried out to evaluate the response of the zooplankton communities on different turbulence levels which are comparable to the hydrodynamic conditions in Lake Taihu. Turbulence was the only systematically controlled experimental variable, which was calculated by the root mean square (RMS) velocity. Results showed that turbulence fundamentally shapes the structure of the zooplankton community. The shift from large body crustacean-to small body rotifer-dominated community was observed with increase in turbulence intensities. The critical time of the shift was approximately 3 days. Turbulence also suppressed the zooplankton growth and biomass compared to calm water. These findings suggest that changes in intensity and extent of turbulence in natural aquatic systems, such as those driven by climate change, could have significant repercussions on the biological communities such as the zooplankton.