Quantitative evaluation of ecosystem management is a primary premise to protect regional ecological security, rationally exploit resources, and achieve sustainable development. In this study, we collected information on potential ecosystem service, human influence, conservation for flagship species, and ecological management. We developed an assessment indicator system for quantitative evaluation of ecosystem management in the Giant Panda National Park (Sichuan Area);Sixteen indicators were included. According to the entropy theory, the dataset created by indicators were selected to evaluate disorder or development tendency of the system quantitatively. The results showed the following. (1) Entropy flow of ecosystem management in the Giant Panda National Park was-0.8309, indicating that the degree of order of ecosystem is increasing and the health status is optimum. Entropy flow on five prefectures were positive; the ecosystem tended to be disordered and on the verge of degradation. (2) Negative entropy flow was from the primary industry (agriculture), whereas, the positive entropy was from flagship species conservation and effective environmental management. Entropy flow varied among different prefectures. The system received the maximum value in Baoxing Xian (0.0880) and the minimum value in Jiuzhaigou Xian (-0.1826). Based on rural residents' income and entropy flow assessment, several actions should be carried out as soon as possible.Management experience from demonstration area should be the priority, and it should be applied at hotspot for management, including Pingwu Xian,Baoxing Xian, and Mao Xian.The tradeoff between regional development and conservation should be balanced for management.