Abstract: A rural system is typically characterized by the coupling subsystems of factor, function, and decision in a coordinated and unified way. Function identification of rural elements can contribute to the scientific decision-making and efficient management of the rural communities. However, some factors have posed important driving forces on the unclear main functions and homogeneous development of rural areas. The classification of the rural regions is usually limited to the functional level, but rarely to the factor level in most previous studies. This study aims to clarify the fuzzy orientation of the main function, and then to propose guiding strategies according to local conditions, using the coupling relationship of “factor and function”. 128 villages in Wannian County of Jiangxi Province, China were taken as the study area. A systematic analysis was made on the capital, labor, facilities, resources, and environment of the villages. A multifactor comprehensive method was selected to calculate the advantage index of rural factor allocation. A self-organizing competitive network and an unsupervised algorithm using competitive learning rules were utilized to divide the types of rural factors. An “element-function” linkage matrix was used to identify the types of rural function, and thereby define the differentiated strategies of rural settlements. The results showed as follows: 1) there was a significant difference in the spatial distribution of dominant degree of the comprehensive allocation of rural factors in Wannian County. Specifically, the advantage index in the northeast county was higher than that in the southwest, while that in the north county was better than that in the south. Four categories were divided into the villages with the high, middle high, middle low, and low, advantage index. 2) In the self-organizing competitive network, eight types were also divided into the combination types of rural factors in Wannian County, such as environment and labor dominant type. The same type of villages showed the distribution characteristics of “overall scattered and local agglomeration”. 3) In the “element-function” connection matrix, the types of rural function had identified the production-, life-, and ecological-oriented function villages, as well as the demolition and merger villages in Wannian County. In the villages of production-oriented function, the agglomeration strategy could be established to integrate three industries, while accelerating the industrial transformation and upgrading. In a life-oriented function, the integration strategy could be formulated with the construction of rural complex and the configuration of the health care industry. In the ecological-oriented function, the ecological economy strategy could be selected to build rural tourism and green economy for better communities. A scientific demolition and merger strategy could be utilized to protect the farmers for better agricultural production conditions. This finding can provide a new idea for rural function identification and scientific classification. The theoretical basis can also serve as the rural revitalization and targeted poverty alleviation.