As clan and blood relations are the essential core of rural social attributes, the rise and fall of the main family names in a village not only affects the spatial arrangement of their internal courtyard houses but also influences the overall spatial pattern of the village. Taking Pei Cheng Village as an example, in this study, quantitative analyses, such as those entailing standard deviation ellipse, kernel density, and space syntax, are incorporated to investigate the changes in rural family names’ courtyard houses and the historical context for these changes to reveal the influence of the evolution of courtyard house distribution under a given social structure on the overall spatial structure of the countryside at the micro- and meso-scales. The results in this study show that there is strong aggregation and bonding associated with the main family surname in a village and that such surnames have an important correlation with the village centre and spatial structure formation. Notably, the distribution of the surname-bearing clan courtyard houses has a certain degree of consistency with the spatial pattern of the village, with the main space corresponding to the main family surname, the secondary space corresponding to the secondary family, and the underdeveloped space corresponding to mixed family surnames. On this basis, the spatial system grading of Pei Cheng Village is summarized, providing a fundamental basis for future planning of Pei Cheng Village facilities and other aspects of planning, such as the selection of locations.