Equalization of education facilities, which means the balanced distribution of human and material resources under limited resource conditions, is one of the goals of sustainable development. In the process of rapid urbanization in China, there are apparent discrepancies between urban and rural areas because of different land and household registration systems. Primary schools with three types of different administrative affiliations also have significant distinctions. This study is aimed at assessing and comparing the configuration of primary schools with three different administrative affiliations, including cities, towns, and villages. After building an indicator system, the entropy weight method is applied to calculate the overall and category configuration scores of each school. Based on a spatial database, the ArcGIS thematic maps display the geography characteristic of each school in different geolocations. Moreover, the Kruskal–Wallis test identifies if the configuration of primary schools with different administrative affiliations is equal. The results indicate that the allocation of primary schools with three different administrative affiliations showed a ternary development. Moreover, although primary schools with city affiliation had significant advantages in education quality and convenience, their supply–demand conditions were not optimistic. In addition, the quality of the primary schools subordinate to towns was better, but convenience was generally lower. Finally, the quality of primary schools subordinate to villages and some towns was still poor. The results provide facts and a basis for policymakers to achieve an equity configuration in the sustainable development context.