Assessing and Optimizing Rural Settlement Suitability in Important Ecological Function Areas: A Case Study of Shiyan City, the Core Water Source Area of China’s South-to-North Water Diversion Project

China’s rural revitalization strategy has entered a new stage of development, in which optimizing the layout of rural settlements constitutes both a critical component and an urgent task for promoting integrated urban–rural development. Important ecological function areas play a vital role in maintaining ecological security; however, research focusing on the evaluation and optimization of rural settlement suitability within these regions remains limited, thereby constraining their sustainable development. Accordingly, this paper selects Shiyan City, situated within the core water source area of China’s South-to-North Water Diversion Project, as a case study. From an ecological perspective, a suitability evaluation system for rural settlements is developed, specifically tailored to important ecological function areas. This system integrates ecological factors including geological hazards, vegetation coverage, soil and water conservation, and soil erosion. Utilizing GIS spatial analysis and the minimum cumulative resistance model, the study assesses the suitability of rural settlements within these important ecological function areas. Furthermore, it proposes corresponding optimization types and strategies for rural settlements in such areas. The findings indicate the following: (1) The rural settlements in the study area demonstrate a “large dispersed settlements and small clustered settlements” distribution pattern, exhibiting an overall high-density agglomeration, though their internal layout remains fragmented and disordered due to geographical and ecological constraints. (2) The spatial comprehensive resistance values in the study area exhibit significant heterogeneity, with a general pattern of lower values in the north and higher values in the south. The region was categorized into five suitability levels: high yield, highly suitable, generally suitable, less suitable and unsuitable. The highly suitable areas, despite their limited spatial extent, support the highest density of rural settlements. In contrast, unsuitable areas occupy a substantially larger proportion of the territory, reaching 46.83%. These areas are strongly constrained by topographic and ecological factors, limiting their potential for development, and the spatial layout of villages requires further optimization, with emphasis placed on ecological conservation and adaptive sustainability. (3) Rural settlements are categorized into four optimized types: Urban–rural integration settlements, primarily located in high yield areas, are incorporated into urban development plans after optimization. Adjusted and improved settlements, mainly in highly suitable areas, enhance service quality and stimulate economic vitality post-optimization. Relocation and renovation settlements, including those in generally suitable and less suitable areas, achieve concentrated living and improved ecological livability after optimization. Restricted development settlements, predominantly in unsuitable areas, focus on ecological conservation and regional ecological security post-optimization. This study integrates ecological function protection factors with spatial optimization zoning for rural settlements in the study area, providing scientific reference for enhancing residential safety and ecological security for rural residents in important ecological function areas.