The Ecological Functional Zone of the Upper Yellow River (EFZUYR) is a critical water-catching area in the Yellow River Basin, the ecological security of which affects the sound development of the ecosystem in the entire basin. Recently, significant land use changes have aggravated regional ecological risks and seriously affected the sustainable development of EFZUYR. In this context, this paper provides an in-depth study of the ecological risks caused by land use landscape changes. With the help of land use data and dynamic degree analysis, the land use transfer matrix, and the landscape pattern index, this paper quantifies the distribution trends of land use landscape patterns in EFZUYR from 1990 to 2018. In addition, this research explores the temporal and spatial dynamic distribution characteristics of landscape ecological risks in this functional zone. The research results show the following: (1) The transfer of land use in EFZUYR from 1990 to 2018 mainly occurred among cultivated land, grassland, and woodland, with the transferred area accounting for 87.16% of the total changed area. (2) The fragmentation degree of built-up areas is 0.1097, 0.1053, 0.0811 and 0.0762 in 1990, 2000, 2010 and 2018, respectively, with a decreasing trend. The dominance degree of grassland has been maintained at the highest level for a long time, with all values above 0.59. The separation degree and the interference degree of built-up areas were the highest and the values of the four periods were above 1.2 and 0.44, respectively. The loss degree of water was the highest, with a value above 0.67, while the value of other land use was mostly below 0.4. (3) The landscape ecological risk of EFZUYR presented a fluctuating rising, falling, and then rising trend. The spatial distribution characteristic of EFZUYR presented “high in the north and south, low in the middle.”, which has been maintained for a long time. The proportion of low-risk areas is as high as 70%, and the overall ecological risk of the region was low. However, the ecological risk of some areas, such as Linxia City and Magu County, increased. These findings can provide theoretical support for land use planning and achieving sustainable development of EFZUYR.