Traditional villages (TVs) are physical manifestations of traditional culture, and their spatial structure embodies the essence of regional culture. The spatial form of TVs in the Ando Tibetan area can be used to understand the historical evolution, turnover, and inheritance of traditional culture in the region. This study uses four typical TVs in the Huangnan Prefecture (HNP). Using the fractal theory, spatial syntax theory, GIS, and geomorphological statistical analysis, this study analyses the spatial morphology structure of TVs of the Huangnan Tibetans. Analyses are conducted from the perspectives of external morphology and internal structure. A quantitative system of spatial morphology of TVs is constructed. This study found that three out of the four sample villages in the HNP have high fractal values (>1.5046) and belong to the strongly structured agglomeration morphology regarding overall morphological characteristics. Furthermore, the public space patches exhibit a more complex spatial morphology and typical fractal characteristics. The morphological characteristics of the village boundaries in the four sample villages exhibit band-like, mass-like, and point-like characteristics. The types of belt and mass tend to point to Muhesha (MHS), JaJia (JJ), and Shuangpengxi (SPX), while Tufang (TF) does not exhibit a clear tendency. The over-spatial permeability of the village is poor, making it hard to perceive the overall space. The average depth, degree of integration, and village selection are concentrated in the central area and the primary and secondary roads. The geometrical center is the core of the village's degree of integration. This study presents traditional Ando Tibetan villages' complex and diverse spatial morphology, providing scientific references for their protection, development, and utilization.