We constructed mass-balance models for the Wuli Lake ecosystem for 2006 and 2009 using Ecopath model. Using these models, we compared changes in ecosystem structure and energy flow before and after implement of the Aquatic Environment Improve Oriented (AEIO) fishery in Wuli Lake. The models included 17 functional groups covering the main trophic flow of the Wuli Lake ecosystem. These functional groups included large culters, other piscivores, Tapertail anchovy, common carp, Crucian carp, Bighead carp, other wild miscellaneous fishes, Silver carp, herbivorous fishes, macrocrustaceans, molluscs, other benthos, zooplanktons, submerged macrophytes, other macrophytes, phytoplanktons, and detritus. The scale of the Wuli Lake ecosystem expanded following enhancement of biological filter-feeding fish and shellfish. The development degree of the ecosystem was increased, as was the efficiency of energy transfer between trophic level. There was an expansion in niche overlap between filter-feeding fish and shellfish and the other functional groups. The relationship among the function groups strengthened between 2006 and 2009, but the ecosystem was at a developmental stage. The rate of material flow and material recycling has decreased.