The three dimensions of ecological, economic, and social vulnerability in the mountainous countryside are caused by the fragility of the natural ecosystems of the mountains, which overlap with the geographical location of the countryside and are associated with farm production and low productivity. This study conducts a vulnerability evaluation of mountainous rural areas based on the fundamentals of ecological vulnerability in mountainous regions by combining “RS and GIS + multistage land use/land cover change (LUCC) + rural vulnerability evaluation theory and quantitative and practical techniques”. The goal of this project is to establish a comprehensive evaluation system that takes into account the various vulnerability levels in rural areas. It is based on the results of the three phases (2000, 2010, and 2020) of land use/land cover remote sensing images of Yunnan Province. The Delphi approach was used to determine the indicator weights. In order to quantitatively assess the rural vulnerability of 129 counties in Yunnan Province in 2000, 2010, and 2020, as well as to reveal the spatiotemporal characteristics of the rural vulnerability of the entire province in each county from 2000 to 2020, the qualitative comprehensive analysis method and the quantitative multi-index comprehensive evaluation method were organically combined. This paper’s objective is to offer a basis for the strategic planning and management of sustainable rural development and revitalization in mountainous provinces. The findings demonstrate that the ecological, economic, and social vulnerability levels all dramatically decreased over the previous two decades in rural Yunnan Province and its counties. The overall vulnerability of rural areas has been somewhat diminished, with an average annual decline of 1.17% over the past 20 years in the whole province. This demonstrates how the construction and development of rural areas over the past two decades have significantly decreased the overall vulnerability of rural areas. There are, nevertheless, substantial geographical variations. At present, the levels of ecological, economic, social, and overall vulnerability in rural areas of Yunnan Province are high.