The estimation of ecological service system value of water resources in Tarim river basin is of great significance for resource allocation management and ecological protection. However, there is still no unified and complete evaluation method for ecological service system value of inland river in China. Based on the perspective of the whole value chain, the study classifies its ecological service functions, and divides 11 sub-categories into 4 categories (supply, regulation, culture and support) as evaluation indicators to carry out quantitative evaluation. The results showed that the total value of ecological service system in Tarim river basin in 2018 was 4156.5247×108 Yuan, and the value of regulating function, cultural function, supporting function and supply function were successively from high to low, which were as follows: 2565.6825×108 Yuan, 1009.5471×108 Yuan, 884.0770×108 Yuan, 20.3350×108 Yuan, among which the value of regulation function is dominant.