Assessing the vulnerability of rural settlement systems from a socio-ecological perspective is helpful to clarify the factors that affect the development of rural settlements, and establish an analytical framework to cope with risk perturbations, and guide the sustainable development of rural communities. Taking the Mengwa flood storage area as an example, this study comprehensively utilized the Vulnerability Scoring Diagram (VSD) framework, the Spatially Explicit Resilience-Vulnerability (SERV) model, and the Bayesian network model to measure regional vulnerability and explore the main factors affecting vulnerability. The results showed that (1) The exposure of rural settlement systems in the Mengwa region exhibited a spatial pattern of "low on both sides, high in the middle, and locally prominent". The sensitivity of rural settlements around the town was relatively prominent, and the administrative villages where the town is located had shown good adaptability. However, the overall vulnerability of the rural settlement system was high and the difference between high and low values was large, the spatial pattern showed an uneven distribution trend, and the structural differences were significant. (2) This study used a combination of qualitative and quantitative methods to categorize the vulnerable zones into three types:low and medium vulnerability zones, sensitive-adaptive high vulnerability zones and sensitive high vulnerability zones, and analyzed the influencing factors of high vulnerability zones based on the Bayesian network. The rural settlements in the Mongwa region are predominantly of the highly vulnerable zone type, the sensitive-adaptive high vulnerability zone was mainly located in the northern and central part of the Mengwa area, where the disaster prevention and control factor had the most significant effect on the probability of rural settlement revitalization, and its construction and development activities were more restricted by the natural environmental conditions, it was not suitable to start the layout of rural settlements, and it should be classified as an ecological protection space for gradual migration and relocation. On the other hand, the sensitive and highly fragile zone was mainly located in the southern valley of Mengwa area, with relatively good construction and development foundation and the greatest influence of topographic and geomorphological factors on the probability of rural revitalization. In order to avoid the aggravation of the decline of the countryside in this area, the number of population, the economic scale and the mode of production should be strictly controlled so as to balance the contradiction between development and protection as far as possible.