Ecological science focuses on the structure and function of the natural environment. However, the study of ecological environments primarily focuses on single-element research and lacks a comprehensive perspective. To examine ecological environmental trends on different scales, the present paper selected Yunnan Province as the study area. Chemical oxygen demand, rocky desertification, forest coverage, natural disaster data and spatial analysis methods were used to obtain the ecological environmental characteristics of each county and construct a comprehensive evaluation method of the ecological environment. The present paper revealed that the environmental capacity in Yunnan Province was at a moderate level, the ecological environment fragility was remarkable, the significance of the ecological environment was very high, natural disasters occurred frequently, and spatial differentiation between ecological environments was obvious. The province may be divided into three functional areas: the comprehensive-balanced area, the efficiency-dominated area and the environment-dominated area. Central Yunnan was a key development zone and the main area for the manufacturing and service industries, which were built as a modern industrial system in Yunnan Province. The ecological environment in northwestern Yunnan and southern Yunnan is of high significance, and this region was an ecological environment protection area that was important area for the construction of the modern agricultural system in Yunnan Province. To achieve sustainable development of the ecological environment, the spatial characteristics of the ecological environment must be determined at the county scale.