It is of great significance to study the trends and internal differences of eco-efficiency in the Yellow River Basin for ecological protection and high-quality development of the Yellow River Basin. According to the characteristics of the Yellow River Basin in China, the eco-efficiency evaluation system was constructed, and the super-efficiency slack-based measure (SBM) model and the super-efficiency SBM model of undesired output were used to calculate the eco-efficiency levels of provinces in the Yellow River Basin from 2005 to 2020, and the variation trend and internal differences were analyzed. The results show that when only the expected output was considered, the eco-efficiency of the Yellow River Basin as a whole and each province showed a fluctuating upward trend, but there were obvious differences. Qinghai Province, Sichuan Province, and Ningxia Autonomous Region had high eco-efficiency, while Shaanxi Province, Shanxi Province, and Inner Mongolia Autonomous Region had low eco-efficiency. Compared with only considering the expected outputs, eco-efficiency of Qinghai Province had improved significantly when considering non-expected outputs. The eco-efficiency of Shandong Province and Henan Province had improved significantly after 2016, while the eco-efficiency of the two provinces had decreased significantly before 2016. The eco-efficiency of Shaanxi, Shanxi, Inner Mongolia, Ningxia, and Gansu had declined to varying degrees. Finally, the reasons for the differences in eco-efficiency in various provinces in the Yellow River Basin were analyzed, and suggestions for improving the eco-efficiency of the Yellow River Basin were put forward.
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