Environmental pollution in the Yellow River Basin and its high-quality development have become important issues of domestic concern. China has formulated a series of environmental protection policies to respond to the ecological degradation of the Yellow River Basin. In this regard, this article used ecological compensation policies to construct a quasi-natural experiment, and took A-share listed manufacturing companies in the Yellow River Basin from 2005 to 2019 as the research objects. A multi-period difference-in-differences(DID) method was used to empirically test the impact of ecological compensation policies on the high-quality development of the manufacturing industry in the Yellow River Basin. It was found that the implementation of ecological compensation policies promoted the high-quality development of the manufacturing industry in the Yellow River Basin, and there was obvious regional and property rights heterogeneity. Specifically, the promotion effect on the high-quality development of the manufacturing industry in the upper reaches of the Yellow River Basin and state-owned enterprise was much significant than that on the middle and lower reaches and non state-owned enterprise. Corporate social responsibility and government subsidies were identified as important ways to promote the high-quality development of the manufacturing industry in the Yellow River Basin through ecological compensation policies. The above research conclusions were robust after undergoing PSM-DID, replacing the explanatory variables, and placebo tests. The study fully considered the channels through which ecological compensation policies played its role in different regions of the basin, which was conducive to improving the ecological compensation policy and realizing the effectiveness of ecological compensation in ecological governance and high-quality development of the Yellow River Basin.