In the context of regional coordinated development and modernization of ecological and environmental governance capacity, the spatial collaborative governance of transboundary river basins has received extensive attention, but the ecological compensation of river basins is faced with the intertwined relationship of rights and responsibilities, and the horizontal ecological compensation mechanism has not yet been perfected. Based on the emergy ecological footprint model, the ecological compensation amount of 90 cities in the Yellow River Basin in 2007-2021 was measured, and the spatiotemporal pattern, regional differences, and dynamic evolution characteristics of distribution were explored by combining exploratory spatial data analysis, Dagum Gini coefficient, kernel density estimation, and spatial Markov chain analysis. The results showed that: ① The spatiotemporal pattern of ecological compensation in the Yellow River Basin was different, the ecological compensation amount decreased slightly in the fluctuation and increased from the northwest to southeast gradient in general, and the high-value areas were concentrated in the areas with a superior ecological background or developed economy, and some upstream cities had given up many development opportunities to maintain the ecological security of the Yellow River Basin, however, failed to obtain reasonable ecological compensation. ② A significant positive spatial agglomeration phenomenon was observed in ecological compensation and the overall spatial distribution trend was "cold in the north and hot in the south." The number of low-payment areas and low-compensation areas gradually decreased, showing a gradually shrinking agglomeration layout from the periphery to the center, whereas the number of high-payment areas and high-compensation areas continued to increase and formed a spatial evolution characteristic of the coexistence of scattered distribution and group distribution. ③ The overall regional differences in ecological compensation expanded. The over-variation density was the main source of the overall differences, and the focus on alleviating the intra-regional and inter-regional differences was located in the downstream areas. ④ A slight multi-level differentiation phenomenon was present in ecological compensation. The influence of different neighbors on the horizontal transfer of ecological compensation was quite different. This spatial spillover effect easily formed a "space club convergence" phenomenon within a certain geographical spatial range, but with the expansion of time, the probability of maintaining the original level of ecological compensation in each city decreased, and mobility gradually increased. Therefore, increasing the investment in ecological compensation in different fields, strengthening the coordinated development between regions, and giving full play to the spatial spillover effect are important ways to solve the current spatial imbalance of ecological compensation in the Yellow River Basin.
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