Setting a scientific and reasonable water quality target is the basis for water quality target management for water bodies such as rivers and lakes. The purpose of this study is to develop a dynamic water quality target setting approach on multiple time-scales for subzones of Lake Taihu in China. This approach is based on the ecological principles of self-organizing adaptation and that the ecosystem structure is decided by environment conditions. Monthly flow scenarios of main tributaries and pollutant concentration scenarios of each of the eight subzones of Lake Taihu were designed firstly. These scenarios were then fed into the EcoLake model to simulate the evolution of water ecosystem variables. A water quality target optimization model was set up to identify the best pollutant concentration scenarios. The optimization model uses algal biomass and submerged plant biomass as optimization metrics. The optimization model was integrated to the EcoLake model lastly to determine the best control targets of total nitrogen, total phosphorus, ammonia nitrogen and permanganate index. The results suggest that the water quality target set in this study is more advanced in terms of promoting water ecosystem condition and supporting fine water environment management for Lake Taihu, comparing to traditional water quality target.