In the process of rapid urbanization, rural settlement space in China is undergoing drastic differentiation and reorganization, and the spatial optimizing and restructuring of rural residential land is conducive to rural transition and development. Based on the theory of system science, this study analyzed the spatial system formation mechanism of rural settlements in characteristic villages, put forward the restructuring framework of "orderly development, focusing on cultural heritage, and based on material conditions". Taking Bamei Village of Jiangkou County, Guizhou Province as an example and using the methods of scale index, gene analysis, and spatial analysis, the internal and external characteristics of the rural settlement system at the village level was identified, and the restructuring modes were proposed. The study found that: 1) The agents of action, cultural genes, and residential buildings constitute the internal system of rural settlements in Bamei Village, and show the characteristics of "multiple agents of action-induced spatial changes, rich cultural genes but poor continuity, and diversified land use structure and function". 2) The external characteristics of the rural settlement system in Bamei Village are reflected in the constraining and guiding role of the external environment to settlement development, which is manifested as distance-attenuation from point or linear infrastructure sites and rivers—the shorter distance to these spatial features, the larger the number and scale of settlements in the village. 3) Based on the feature cognition and restructuring framework and the partition-classification method, this study divided the village into four zones of management including the core zone, the key zone, the promotion zone, and the conservation zone, as well as four residential upgrading types of intact, damaged, missing, and distorted, and proposed the spatial restructuring strategy of rural settlements under two organizational modes.