Abstract: 11 counties in Huaihe River Source area were selected as the research objects and the regional ecological compensation standard was studied by using the method of ecological value and land carbon emissions method. The ecological compensation was obtained from these two accounting methods in the range of standard and reference. Meanwhile, according to the economic development level of each county, the eco-compensation priority sequence was quantified and partitioned. The purpose was to solve the standard and object for compensation. The results showed that the upper and lower bounds for ecological compensation were 222.64 and 64.84 billion yuan, respectively, and Shangcheng county possessed the greatest ecosystem services value, but Huaibin county was the opposite. Furthermore, all regions of Huaihe River Source belonged to carbon sink area. Moreover the priority level of ecological compensation expressed the descended distribution trend from south to north. Thus the investigation provided scientific foundation and decision-making support for the key ecological function areas of the Huaihe River Source.