Abstract: In ecological resettlement area, there are complex conflicts of interest among different groups in terms of ecological environment protection. It is an important task of ecological risk mana-gement to construct a decision-making model accordingly, taking into considerations of the stakeholders’ knowledge of category and interference intensity in ecological resettlement area. This paper categorized migrants in ecological resettlement into four different interest groups in accordance with stakeholder theory, and adopted participatory semi-structured interview and qualitative polymerization to build an ecological risk factor system with 3 primary variables and 13 secondary variables. Besides, the ecological risk identification was further carried out by utilizing Fuzzy Cognitive Map (FCM) and Artificial Neural Network (ANN) model. The cognitive results of stakeholder groups revealed that the garbage pollution risk variable was most widely mentioned by different interest groups. In the meanwhile, obvious differences existed among stakeholder groups on ecological risk variables. The managers paid attention to the formulation of environmental protection and the implementation of the policy; the residents were concerned about the improvement of the living standard, which was directly related to the environmental consciousness and behaviors; most of the operators pursued economic interests and environmentalists focused on the eco-environmental problems. The graph theory index of stakeholder groups showed that the managers and environmentalists were more comprehensive and clear with regard to the understanding of ecological risks in resettlement areas. The overall risk cognition results of all the stakeholders in the resettlement area revealed that the ecological environmental risk factors significantly affected the safety and satisfaction of residents, and the public policy played a major role in the risk management of resettlement areas. The centrality of risk variables further showed that improving the living standards was the key to prevent ecological risks. The results of ecological risk perception and management scenarios showed that solving the problem of garbage pollution could improve the ecological environment, and the key was to ameliorate and implement the relevant public policies; establishing and improving the social security system was directly related to the living standards of residents and environmental protection behaviors; and strengthening infrastructure construction would affect the landscape ecological pattern, biological habitat and biodiversity, and improve residents’ satisfaction and public participation.