Evaluations connect ecosystem and human welfare to achieve restoration. There have been an increasing number of studies conducted on various ecosystem service assessments, but little research has focused on inland river basins playing a critical role in development in northwestern China. The distinct differences in natural endowment, socioeconomic characteristics among the upper, middle and downstream inland river basin require heterogeneity during evaluation. The objective of this study was to verify the existence of population preference heterogeneity and examine impact factors using choice experiment surveys in the Shiyang River Basin, China. A mixed logit model using data from 714 households across the entire basin estimated mean willingness to pay and the standard deviation for ecological attributes. Ordinary least squares (OLS) was employed to estimate the effects of exogenous variables on all willingness to pay estimations. The results demonstrate that ecosystem service values are heterogeneous among people. Willingness to pay is affected by personal and regional characteristics. Government involvement will be required to seek differentiated ecosystem services values among populations and facilitate public support.