The basic characteristics of mountain areas are that the innate ecological environment is relatively fragile, the acquired ecological environment is severely damaged and degraded, the whole economy and society are still relatively backward, and the degree of sustainable development is relatively low. At present, it has not been seen that land use sustainability evaluation (LUSE) research lasting for many years based on RS and GIS in mountainous provinces. It is urgent to build a suitable, feasible, operable and applicable LUSE system for mountainous regions so as to provide a basic foundation for strategic planning and management of sustainable land use in mountainous provinces. This study integrated “RS and GIS + multi-phase LUCC + LUSE theory and quantitative practical methods” based on mountain provinces, firmly grasped the basic characteristics of mountain areas—the vulnerability of ecological environment, and conducted the study on mountain LUSE. According to the outcomes of RS of land use in the study area in three phases (2000, 2010 and 2020), a comprehensive indicator system is established from the three dimensions of ecological friendliness of land use (EFLU), the economic viability of land use (EVLU) and social acceptability of land use (SALU). Using the Delphi method to determine weights and combining the AHP method and the comprehensive analysis method, this paper quantitatively measures the overall sustainability of land use (OSLU) of 129 counties in Yunnan province in 2000, 2010 and 2020, revealing the spatio-temporal characteristics of the OSLU of Yunnan province and all counties from 2000 to 2020, and aiming to provide a basic and foundation for strategic planning and management of sustainable land use (SLU) in mountainous provinces. The degree of ecological friendliness (DEF), degree of economic viability (DEV), degree of social acceptability (DSA) and degree of overall sustainability (DOS) in Yunnan province and all counties have been significantly improved. Accordingly, the OSLU has been improved to a certain extent, with a 0.66% annual growth rate. It indicates that the development and construction from 2000 to 2020 have significantly improved the OSLU. However, regional differences are large. At present, EFLU, EVLU, and SALU in Yunnan province are not high as a whole. The basic situation reflected that there are obvious deficiencies in EFLU, EVLU and SALU in Yunnan province. Land exploitation and use activities have caused certain influences and the destruction of the ecological environment.