Ecosystem health assessment is one of the most important issues in regional ecological quality and safety studies. It also has a great significance to ecological conservation and regional development. This study focused on assessing the health status of forest, agriculture and urban ecosystems in the southwestern Beijing, China, including the Fangshan and Fengtai Districts. Based on field surveys and data collection, an assessment index system containing the vigor, organization and resilience factors was developed to measure the ecosystem health. Each index was scored from 1 to 5, representing five levels that contribute to the whole ecosystem health. The analytic hierarchy process (AHP) method was used to measure the weights of each index and three factors, and thus an overall score for a certain ecosystem was calculated. The results show that the forest ecosystem in the Fangshan District had higher health value than the Fengtai District, while the urban ecosystem had a slightly lower value in the Fangshan District than the Fengtai District. Both districts show lower resilience values in forest and urban ecosystems. Maintaining the ecosystem health will definitely benefit the long-term development of two districts. This study suggested that an approach for assessing the regional ecosystem health could be further developed to address spatial and synergy relationships between ecosystems and the three health factors.