Abstract: The morphology of island settlements reflects the organization and evolutionary patterns under unique habitat environments, and their growth drivers still need to be scientifically studied. In this paper, 53 rural settlements on Nantian Island, Xiangshan County, Ningbo City, are studied, in which mountainous settlements exhibit significantly different vertical morphological features from those on the plains due to the complexity of the terrain. However, current research generally lacks a comprehensive quantitative method for the three-dimensional morphology of settlements. In order to fill the research gap, this paper innovatively introduces vertical spatial indicators on the basis of the traditional two-dimensional planar spatial morphology study of settlements, and constructs a three-dimensional morphology quantification index system for mountain settlements on islands. At the same time, the cluster analysis method is used to classify the spatial morphology of settlements, and the influence of natural geography and socio-economic factors on the morphological characteristics of settlements in mountainous island is explored in depth. On this basis, spatial development strategies for the protection of settlement patterns are proposed, which provides a new perspective and direction for the protection and sustainable development of rural settlements in mountainous island regions.