Wetland is one of the most important ecosystems on earth. They provide a wide variety of ecological services, including nutrient cycling, carbon storage, flood reduction, provisioning of habitats for wildlife as well as ensuring water supply, food security and livelihoods for people living in developing countries. The aim of this paper is to better understand the economic value of wetland and the services it provides to humanity and to offer a basis for policy and decision making and sustainable development. We take the wetland in the National Nature Reserve located at the Heihe River basin as a case study and collect data from field investigation. We assess the direct ecological service values (ESVs), i.e. biological production and industrial raw material, and indirect ESVs including climate regulation, flood adjustment, water supply, pollutants degradation, habitats providing, carbon sequestration and oxygen release and the value of recreation and culture, of the wetland ecosystem, using some mathematic and economic methods, such as market value method, the shadow engineering method, carbon tax method, ecological method and travel cost method. Results from this study showed that: wetlands in the Heihe Reserve which cover an area of 41164.56 hm², are divided into natural and constructed wetlands, including river wetland, swamp wetland, lake wetland, aquaculture pond, irrigated land, water reserve, and salt pan and so on, 13 categories in total. The average ESV of the wetland ecosystem in the Heihe reserve was about 3 289 million Yuan per year. Of the total ESV, the annual value of flood adjustment was 1086 million Yuan, followed by the value of carbon sequestration and oxygen release being 673 million Yuan. The annual values of recreation, water supply, climate regulation, habitats provisioning, culture and pollutant degradation are 420, 380, 329, 101, 97 and 25 million Yuan, respectively. The direct ESV of the wetland ecosystem, namely industrial raw material production, is 178 million Yuan per year, which account for 5.4% of the total ESV. The results indicated that the ESVs of wetland is huge and indirect value is substantially greater than the direct value, which suggests that we should attach great importance to the significance of wetland's ecosystem service functions in ecological construction practices in river basin in desert area of China. We expect our study could help to cover the shortage of enough knowledge of service value of wetland ecosystem in arid regions thereby promoting the exclusion of blind development,irrational utilization and severely damage of the ecological environment, and achieve sustainable regional development.