With the rapid development of the economy and the intensification of human activities, ecological systems have been degraded, especially in arid areas. The lower reaches of the Tarim River represent a typical arid area in China. Since 2000, the Chinese government has been heavily investing in the protection and restoration of the natural ecological environment of the lower reaches of the Tarim River. In this study, we aimed to resolve two key scientific issues: (1) reveal the changing characteristics of land-use in the region and identify the changes in ecosystem service value caused by these land-use changes and (2) evaluate whether the environmental quality has improved or worsened. The objective of this study is to verify whether the ecological water conveyance project promotes an increase in the ecosystem service value, with an improvement in the ecological environment, to thereby provide references for the evaluated effects of ecological water conveyance for the management of water resources. In this way, economic development can support environmental protection. Thus, the economy can be sustainably developed. Hence, based on the remote sensing data of land-use in 1990, 2000, 2010, and 2016, with the value coefficients proposed by Constanza in 1997 and changing characteristics in the land-use, the ecological service value, and environmental conditions from 1990 to 2016 were analysed. According to our results, from 1990 to 2016, the ecosystem service value has increased substantially, indicating that the benefits of ecological water conveyance were significant. The environmental condition index increased by 21.14%, showing that the ecological environment has improved. However, the environmental quality remained low. In the future, we should formulate plans for reasonable land-use that control the replacement of woodlands and grasslands with farmlands and construction. The results of this study provide a scientific basis and practical guide for restoring inland river ecosystems in arid regions.