Carrying out an ecosystem health assessment and building an ecological safety network are essential measures to effectively manage ecological capital and protect biodiversity, especially in eastern Yunnan, where rocky desertification is widespread, and the ecological base is weak. Besides, they can prevent potential ecological risks and ensure ecological safety. In this paper, ecosystem services were incorporated into the ecosystem health model, and an ecological security evaluation system of "vitality-organization-resilience-ecosystem services" was constructed and quantitatively evaluated the ecosystem health status of Qujing City from 2000 to 2020 and identified the core areas accordingly. With the help of the sensitivity of rocky desertification, the resistance surface based on the land type was modified. The minimum cumulative resistance model and gravity model were used to identify the ecological corridors and build the ecological security network of Qujing City. The results showed that:(1) during the study period, the ecosystem health status of Qujing City increased and then decreased, indicating a downward trend. Except for the urban built-up areas significantly affected by human activities, the ecosystem health status in the other regions was generally stable. (2) The core areas of Qujing City were 8656.65 km², accounting for 29.92% of the study area, and the coincidence rate with the nature reserve was 70.18%, with an irregular distribution from northwest to southeast, and concentrated in the north and southeast of Qujing City. (3) There were 143 potential corridors, 137 ecological nodes, and 82 ecological breakpoints distributed in a network radiation pattern. The southwest was not actively distributed with corridors, which was easy to form an ecological island, and the regional connectivity needed to be improved. The ecological network considering the sensitivity of rocky desertification could better reflect the resistance when species migrated, and the ecological corridor could realize the connection between different sources. This paper paid close attention to the characteristics of the environmental conditions in eastern Yunnan's karst ecological fragile area. It constructed a mountain ecological network pattern that considered the sensitivity of rocky desertification. It could provide a new idea for optimizing the ecological network of small and medium-sized cities with similar environmental backgrounds.