Sanjiangyuan Region is the headstream area of three main rivers in Asia, i.e. Yangtze River, Yellow River, and Lancangjiang River (Mekong). It is an important ecological barrier of the local and regional environmental security and sustainable development, not only for China but also for the southeastern Asian, In recent decades, however, grasslands in Sanjiangyuan Region were seriously disturbed or destroyed by both global climate change and human activities, which led to sharp decrease of nourishing capacity of source water and serious environmental problems of the lower reaches. Since 2005, Chinese government began to implement a series of activities, e.g. ‘Returning Grazing Land to Grassland Project’ and ‘Ecological Migration Project’, in Sanjiangyuan Region to alleviate the situation of grassland degradation, and gradually restore and protect the ecological environment. The success of such projects in Sanjiangyuan Region depends largely on local herdsman's active response, support and participation,however, the herdsmen's well-being improved or nondecreased is the key to the effective implementation of ecological protection and herdsmen's participation willingness directly influences the accomplishment efficiency and sustainability of ecological protection.Based on the framework of Sen's function and Maslow's hierarchy of needs, this paper states the connotation of the well-being and constructs the evaluation system of well-being. The participatory rural appraisal methods were employed to survey the 159 herder household in Maduo County in the source region of the Yellow River. Based on the questionnaire survey, the fuzzy and analytic hierarchy process were used to determine the weights, this paper evaluates the well-being of Maduo herdsman before and after they participated in the protection of natural resources, then analysis the behavior response. The results indicate: (1) The connotation of human well-being in the protection of natural resources is that the freedom and ability of human when they choose their life, while they want to achieve a better life, health, experience, a variety of social relationships, a sense of belonging, respect and self-worth in the production and utilization of human ecosystem. Poverty refers to the limited capacity and development; it also means the decline in well-being. (2) Well-being is multidimensional and hierarchical, and the degree of realization of low-level functional dimension will affect the realization of the high-level functionality dimension, ultimately affects the well-being of the individual. (3) The individual value of Maduo herdsman in the migrant of ecological protection deceased from 5.061 to 4.708, the loss of well-being is caused by constraints of livelihoods capacity, and results in low-level demand of income and consumption cannot be satisfied, then affects the achievement of high-level function such as the realization of life implementation and self-worth and a sense of belonging. Especially the migrant whom part cited in the protection of natural resources cannot continue to live in the grasslands, the ability and development right has been limited, which led to the decline of well-being. (4) We should pay attention to the well-being of the herdsman, whom strongly dependent on grazing in the grassland ecosystem, then understand and in-depth analysis of the response mechanisms and driving force of herders' ecological protection behavior, and establish scientific ecological compensation mechanism which based on well-being losses, that the ecological protection and social well-being will be balanced and maximized. (5) For the purpose of enhance human capabilities and promote the diversification of herdsman' livelihoods to improve the well-being and incentive the herders actively involved in ecological protection, the natural resource conservation and management planning should be formulated under the concept of sustainable development, which can achieve the effective ecosystem protection -improve human well-being -the development win-win situation.