Analyzing the survival and development environment, internal dynamics, and development direction of specialized farmers’ cooperatives in underdeveloped areas to enhance the vitality of the development of the agricultural industry is a key strategy for the work of the “Three Rural Issues” in China. Based on the data of 3194 specialized farmers’ cooperatives in Yunnan Province from 2000 to 2023, this paper utilizes the spatial measurement method and survival analysis method to study the spatial distribution of their survival and related influencing factors. The study found the following: (1) Cooperatives show a spatial aggregation trend from “high to high” to “low to high”, and the formation of new sub-core areas is accelerating. (2) The establishment stage of cooperatives shows an obvious annual cycle effect, and cooperatives established in the early stage show stronger survival resilience. (3) The factor of “organizational characteristics and technological innovation” significantly prolongs the survival time of cooperatives, while the factor of “establishment stage” has a negative effect. (4) The influence of a cooperative’s asset size and trademark on its operational durability tends to decrease over time, but the influence of relatedness remains relatively stable. (5) Over time, the survival and development patterns of cooperatives at the provincial level show obvious differentiation, and the clustering phenomenon of “low-high” development gradually appears in minority autonomous counties. The results of this study provide a scientific basis for deepening and strengthening the study of the basic rural business system.