Abstract: The Yellow River basin is an important ecological safety barrier, an agglomeration area of resource and energy, and an area with highly intensive production activities in China. Therefore, its ecological change directly affects the sustainable development of the ecological environment and economy in the basin. This paper aims to quantitatively assess the ecological vulnerability and analyze the spatial heterogeneity in the Yellow River basin. To this end, an evaluation system was established using the partition-integration assessment method by selecting indicators such as water resources, climate, soil, vegetation, and human activities. Meanwhile, a multiplication model was introduced. The assessment results are as follows. The overall ecological environment in the basin is moderately vulnerable, with moderately vulnerable areas accounting for 42.37% of the total area of the basin. Meanwhile, the areas with a highly vulnerable ecological environment in the basin are mainly distributed in the urban economic belt along the upper mainstream of the Yellow River. From 2000 to 2018, the ecological vulnerability of the basin first decreased and then increased. During this period, ecological problems were the most notable in 2000 and ecological vulnerability was the lowest in 2015, with the Comprehensive Vulnerability Index (CVI) of 2.28 and 2.00, respectively in 2000 and 2015. The ecological vulnerability and its evolution trend in the basin significantly varied in space. In detail, the ecological vulnerability notably increased in the plateau areas in the upper reaches, slightly changed in the urban belt along the river, and significantly decreased in the middle and lower reaches.