Education is the driving force of social development, while regional differences have restricted the balance of educational development. This paper provides a political and geospatial analysis of regional inequality across the province from 1990–2015 under a comparative spatiotemporal conceptual framework. Great differences in terms of the distribution and dynamic changes in primary school were found between southern and the northern Ningxia. The southern region has a large number of primary schools with a sharp reduction in these numbers, especially in recent years, while the north has a small but stable number of schools. Spatial accessibility analyses revealed that due to the imbalance between the south and the north, the spatial accessibility of the southern region is much worse than that of the northern region. Our study found the imbalance in the number and spatial distribution of primary schools in the north and south of Ningxia was formed because of multiple factors of policy, geography, and social-economy. The government has pursued a policy of promoting education fairness. However, neglecting differences between north and south, on the contrary, has brought negative effects to the south, worsened the educational environment, and increased education inequities. Our case study in the Ningxia district demonstrates that this research can provide a practical basis for the formulation of policies to guide the rational planning of primary education in Ningxia and/or other similar areas.