China’s urbanization has achieved rapid development in the past 20 years, with towns expanding in size and the population increasing, while rural society has also undergone dramatic changes. An in-depth study on the evolution process of rural settlements in the context of rapid urbanization is beneficial to the rational planning of villages and the promotion of green and sustainable urban development. Located in East China, Sishui County is in the transition area between three types of landforms: hills, plains, and mountains. The spatial distribution of rural settlements in the urbanization process shows obvious regional differences. To our best knowledge, research on the spatio-temporal evolution of regional settlements in Sishui County is rare. In this study, we chose Sishui County as the study area, utilized Landsat5 (TM) and Landsat8 (OLI) satellite data as remote sensing data sources, and applied Geographic Information System (GIS) spatial analysis methods, central place theory, and core–periphery theory to explore the evolution process for the pattern, scale, and structure of rural settlements in this region from 2000 to 2021 and to investigate the influencing factors. The results show that: (1) in terms of the evolution of the rural settlement pattern, its distribution shows a gradual increase in the degree of dispersion, which indicates an overall development trend in the region of Sishui County in recent years and that the trend is gradually increasing; (2) in terms of scale evolution, the degree and speed of expansion in rural settlements of Sishui County have gradually decreased, and the scale grade has gradually increased; (3) in terms of structural evolution, the hierarchy system in rural settlements of Sishui County is constantly being improved and optimized from a simple to a complex core–periphery structure. These results will provide data support for the rational planning of villages and sustainable, high-quality urban development. They will also help local governments take appropriate measures to achieve coordinated and sustainable socio-economic and environmental development in the region.