Watershed ecological compensation (WEC) is a popular and effective policy instrument for promoting the coordinated development of environment protection and the regional economy in river basin areas. WEC affects the regional economic differences between upstream and downstream regions, as well as between protected areas and areas surrounding upstream regions. Thus, it is necessary to quantify these changes to ensure the balanced development of regions after the implementation of ecological compensation. In the present study, we established two types of Theil indexes for between-group inequalities (THH and THS) and an intervention analysis model in order to evaluate and predict the effects on regional economic differences caused by WEC in the Xin’an River basin. The results showed that the intervention comprising WEC affected regional economic differences, where the economic gap widened between Huangshan City in the upstream region and Hangzhou City in the downstream region, as well as between Huangshan and its surrounding cities. However, the impacts of the intervention gradually decreased in the later pilot period. Considering the fairness of regional social development, we recommend increasing the compensation for protected areas in order to improve the self-development capacity of upstream regions.
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