Coordination between ecological security and economic development is crucial to sustainable development, with a development strategy that should be adjusted according to the type of region. Yunnan Province, China, is a treasure trove of biodiversity but is economically lagging. Clarifying the relationship between ecological security and economic development can provide a reference for the sustainable development of similar biodiversity hotspots in the world. The landscape index method and index evaluation method were used to calculate the ecological safety index (ESI) and the economic development index (EDI), respectively, and the median value of the indices was used for the comprehensive zoning. The coupled coordination degree model (CCDM) was used to assess the coordination status of ecological safety and economic development in each zone. The results show that (1) Yunnan’s ecological security pattern is high in the west and low in the east, mainly influenced by topography, climate, and human activities; its economic development is resource-dependent and shows a multi-point dispersed pattern due to poor transportation; (2) Yunnan was partitioned into the Coordinated Development Zone (CDZ), the Ecological Risk Zone (ERZ), the Economic Poverty Zone (EPZ), and the Dual Pressure Zone (DPZ). Among them, CDZs (15%) are mostly areas with outstanding advantageous resources, mature characteristic industries, and relatively spatially dispersed. There are two types of ERZs (35%): one is an area where the intensity of human activities exceeds the ecological carrying capacity, mainly located in the eastern plateau; the other is an area with fragile ecological background conditions, located in high mountains and river valleys. EPZs (35%) are mainly lagging in socioeconomics of DPZ (15%) and the fragile ecological environment constrains each to form a negative cycle. (3) Of the regional coordination levels in Yunnan Province, 76% are moderately coordinated, and there is still space for development from the high-quality coordination level. The order of the average coordination degree of each partition is CDZ > ERZ > EPZ > DPZ. The poor basis for coordination and the single approach to coordination have led to ecological safety and economic development often being more difficult to achieve in areas with large mountainous areas similar to Yunnan. (4) Due to the necessity for biodiversity protection, Yunnan Province should choose the sustainable path of ecological priority and green development. Specifically, CDZ should play to industrial advantages and brand effects, and promote industrial integration and innovative industrial development paths. The keys to ERZ are industrial restructuring, industrial ecologization, and ecological environment restoration and protection. EPZ should improve transportation and other infrastructure and revitalize economic development under the premise of ecological priority. Finally, DPZ should emphasize human and load reduction, and moderate development.