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Ecological protection and restoration results in a series of complicated changes in land cover. Lack of research on the historical and potential effects of land cover change on ecosystem service value (ESV) hinders decision-making on trade-offs involved in environmental management. To address this gap, the effects of land cover change on ESV in the upper reaches of the Heihe River Basin in northwestern China were evaluated. First, on the basis of land cover maps for 2001, 2008 and 2015, the land cover map for 2029 was predicted with CA-Markov model. Then, the changes in ESV resulting from land cover change were valuated with the benefit transfer method. The results showed that the total ESV increased from $1207.33 million (USD) in 2001 to $1479.48 million (USD) in 2015, and the value was expected to reach $1574.53 million (USD) in 2029. The increase in ESV can be mainly attributed to expansion in areas of wetland. In this study, the elastic index was applied to identify areas that were more sensitive to ecological management, aiding in selecting sites for investment in ecological protection and restoration programs. Furthermore, the potential effects of land cover change on ESV was evaluated. The results are of great importance for guiding future ecological management.