Rural settlements are the basic spatial units to implement the rural revitalization strategy. However, the weak links of rural settlements are found in the ecologically vulnerable areas, particularly for the coordinated and high-quality development of regional ecology and economy. Taking Tianzhu County in Guizhou Province as the study area, this study aims to analyze the evolution, influencing factors and dynamic variation in the spatiotemporal patterns of rural settlements in the ecologically vulnerable areas from 2012 to 2022 using "Scale-Space-Morphology" approach. The rural settlement patches and administrative villages were then taken as the research objects. Three research nodes were selected in 2012, 2017 and 2022. The optimal parameters were obtained, according to the average nearest proximity index, landscape pattern index and geographical detector. The research procedures were as follows. Firstly, the scale, spatial distribution and morphological pattern of rural settlements were characterized by landscape pattern index, nearest distance value and morphological dimension. The spatiotemporal pattern and evolution of rural settlements were identified in the ecologically fragile areas. Secondly, the optimal scale was obtained for the dispersion of different influencing factors using spatial dispersion and quantitative combination. Finally, the geographic detector model with optimal parameters was used to identify the influencing factors and dynamic variation in the scale, spatial distribution and morphological pattern of rural settlements in the ecologically fragile areas. The results show that: (1) The scale pattern of rural settlements in the ecologically vulnerable areas shared a trend of increasing and then decreasing, which was mainly dominated by micro settlements and small settlements. But the average scale was much higher than the national level. The scale of rural settlements was gradually shifted from the quantitative to qualitative enhancement; (2) There was a significant autocorrelation in the spatial pattern of rural settlements in the ecologically vulnerable areas. The degree of spatial agglomeration was gradually increasing. The layout shared the “four-week to middle core agglomeration” trend, that is, the central and southern regions were formed two larger and multiple smaller agglomeration areas; (3) The outstanding fractal features were observed in the rural settlements in the ecologically vulnerable areas. The evolution of morphological index shared a trend of first rising and then decreasing. But there was the outstanding variation in the stage increase on the whole, together with the simple morphology; (4) There were the unique influencing factors on the evolution of the “scale-space-morphology” pattern of rural settlements in the ecologically vulnerable areas. Generally, there was a trend of transformation from natural conditions to social economy and policy. Among them, the relocation sites for poverty alleviation, transportation accessibility, village and town planning and distance from town centers were the main influencing factors on the spatial and temporal evolution of rural settlements. Especially, the relocation sites for poverty alleviation, village and town planning were defined as the continuous enhancement type. Finally, the targeted recommendations were made to strengthen the territorial spatial planning, ecological protection, the spatial pattern of rural settlements in the production and living of farming households.