Ecological compensation is an effective strategy for promoting regional ecological protection as well as coordinated socio-economic development. Currently, limited interest is garnered for ecological compensation schemes predicated on the flow of ecosystem services. Quantitative assessments remain scarce. Herein, a novel ecological compensation mode based on supply-flow-demand theory of ecosystem regulatory services was proposed to clarify the supply-demand relationship of regulatory services in Yellow River Basin. Combined with analysis on wind field, hydrology and hot spot, the supply area, demand area and transmission paths in between are identified. Through the comparison of service flows stemming from eco-radiation and ecological compensation, encompassing recipient cities, compensating cities, and the compensation amounts, a clear delineation was ultimately achieved for regulatory services within the Yellow River Basin. It was found that (1) The spatial distribution of water conservation and carbon sequestration service supply in the Yellow River Basin in 2020 is "high in the south and low in the north, high in the west and low in the east". The demand distribution is strongly associated with the population density, reflecting "high in the east and low in the west". (2) The supply-demand relationship of water conservation services in the Yellow River Basin is overall in deficit with difficulties in meeting the supply demand. Even though the supply of carbon sequestration services in most areas can satisfy the demand, the warning line for ecological deficit is approaching. (3) 8 recipient cities and 22 compensated cities were determined for water conservation, while the numbers of recipient and compensated cities were 10 and 28, respectively, for carbon sequestration service. The total amount of ecological compensation for ecosystem regulation services in the Yellow River Basin was 67.654 billion RMB, of which 16.054 billion RMB worked for water conservation services, and 51.6 billion RMB acted as carbon sequestration compensation. These results are expected to provide insights for establishing ecosystem management policies and practical application in ecological compensation in the Yellow River Basin.