The health of regional ecosystem is the key element for sustainable socio-economic development and the base for friendly environment. With rapid urbanization, intensification of agriculture, and industrial production, the influence of human activities on regional ecosystems is increasingly apparent. The anthropogenic disturbances of regional ecosystems cause a series of problems:resource destruction, environmental pollution, ecological deterioration, soil and water losses, and frequent disasters. The evaluation of regional ecosystem health has been the hotspot of the present research in ecology. Several indicators have been employed to measure the changes in ecosystem functions, but most of the studies are focusing only on environmental pollutants and economical conditionals, neglecting the nonlinear process involving the comprehensive natural and socio-economic systems at different scales. Based on the theoretical foundation of system science, landscape ecology, and management science, we built a dynamic evaluation system, comprising one object layer, four decision layers, and 16 criterion layers. The key indicators involving the natural, social, and economic data were employed to assess the fitness level of the ecosystem and other four subsystems (social system, environmental system, economical system, and risk system) quantitatively. In the case study, the ecosystem health of the Maoji Biosphere Reserve was evaluated by using the proposed method. Results carried out on a 5-year scale indicated that the health condition of the social system increases but at a modest rate and it is limited by the population health level and the happiness perception intensity. The health condition of economic system soared to 149.5% in just 5 years, but with a significantly negative effect. Two key factors in this subsystem, the comprehensive economic development index (with a weight of 0.0496) and the potential economic development index (with a weight of 0.0454), experienced a 92.4% and 5439.5% expansion, respectively. The health condition of the nature fluctuated 15% in a peak-to-trough pattern, and it was inversely correlated with the risk system. The biodiversity decreased, resulting in the less resilient nature subsystem. Shaking of the comprehensive socio-economic and natural system led to the surge of the risk index in 2011.The health condition of the regional ecosystem belonged to class Ⅲ (ordinary level) each year; positive membership degree first increased and then decreased. These results showed that the study area progressed greatly toward achieving a harmonious society and vigorous economy in the past 5 years. Nevertheless, the stress effect of strong human disturbance on regional ecosystem enhanced the system's sensitivity and landscape fragmentation mainly by the pressure from environmental contamination. The management of the Maoji Biosphere Reserve will focus on the strategies in cultivating the natural endowment of ecology, improving the resistance of the social system, and optimizing the economic structure. Proposed model yields satisfactory results in evaluation of fitness conditions of the regional ecosystem in the study area. This approach plots a time spectrum of regional system change systemically, integrally, and insistently, and it can be applied to assess other similar ecosystems.