Against the backdrop of accelerated globalization and urbanization, traditional settlements in the Jiangnan waterside areas of China face challenges such as morphological distortion and a simplified spatial structure. The ecological adaptability and cultural value of settlements urgently need scientific protection. There has not been enough research on how to better classify settlements, how to conduct systematic morphological analysis, or how to use dynamic protection methods. This makes it hard to fully show the variety of settlement types and how they differ in different areas. To this end, this study uses a combination of GIS spatial analysis, type classification, and case study methods to classify and morphologically analyze 159 traditional settlement patches in the Nanxi River Basin. We construct a settlement type map from quantitative research on topographical, water system, and spatial morphological characteristics, and extract a spatial organization model of mountains and water. The results show the following: (1) The main morphological types, such as the plain–waterfront–strip-shaped and cluster-shaped/finger-shaped types, are typical patterns of traditional settlements in the basin. This indicates how well settlements can adapt to their natural surroundings. (2) This study summarizes six typical settlement sample spaces. (3) The settlement digital protection strategy suggested in this paper uses GIS and 3D modeling technology to make it easier to record, show, and manage information about settlement spaces. This offers a new way to protect traditional settlements scientifically. The study not only enriches the theoretical understanding of the settlement morphology of Jiangnan landscape pastoral areas but also provides an important reference for the protection and sustainable development of settlements in similar basins around the world.
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