In shallow lakes, primary producers are mainly benthic plants and phytoplankton distributed in benthic and pelagic habitats, respectively. The benthic plants include submerged vascular plants and benthic algae. Phytoplankton are mainly consisted of planktonic algae. The benthic plants usually dominate in oligotrophic lakes with low nutrient concentrations and high transparency as benthic plants can access the nutrient resources in the sediments. Due to the increase in external nutrient loading, nutrient concentrations increase and the limitation of phytoplankton by nutrients is reduced gradually. Due to their superior competitive ability in light, phytoplankton become the dominant primary producers in shallow lakes, and the ecosystems shift from a clear, benthic plants dominated state to a turbid, phytoplankton dominated one, i.e. regime shifts. During the process of regime shifts, ecosystem structures and functions of lakes change tremendously. This paper reviewed the changes in sediment properties, and community structures of phytoplankton, benthic plants, macroinvertebrates and fish. The impacts of these changes on the competitive advantage of phytoplankton and benthic plants, exchanges of phosphorus between benthic and pelagic habitats are synthesized. The impact of eutrophication on benthic-pelagic coupling process and the mechanisms of regime shifts in shallow lakes are discussed. There are some important implications for the restoration of shallow eutrophic lakes. The aims of shallow lake restorations are to re-establish the clear water states, and thus the criteria evaluating a successful restoration should include parameters determining clear water states, such as Secchi depth, phytoplankton biomass, benthic plant coverage or dominance. Studying the technology or methods of lake restorations should focus on controlling the major process of benthic-pelagic coupling, such as control of sediment phosphorus release and benthivorous fish, and restoration of benthic plants, specially submerged plants.