The economic values of ecological service functions of Gaoyou Lake, including material production, water supply, water storage, flood drainage, climate regulation, transpiration endothermicity, water purification, scientific and cultural education and maintenance of biodiversity, are evaluated by using the comprehensive methods of economics and ecology. The results show that the total values of 9 ecological service functions of Gaoyou Lake in 2009 are 47.6863 billion yuan, and the direct and indirect ones are 15.2216 and 32.4639 billion yuan, respectively. Among them, the flood drainage, transpiration endothermicity and material production are the top 3 functions, which are 26.77%, 24.05% and 14.21% of the total values respectively. The ecological system of Gaoyou Lake plays an important role in flood drainage, transpiration endothermicity, aquaculture and other aspects, and they are the core service functions of Gaoyou Lake. This study may provide the basis for the ecological restoration, water resources protection and management of Gaoyou Lake.