China’s higher education has entered the stage of a universal system, enrolling over 50% of students, and the Chinese government takes its high-quality oriented development as its educational goal. However, as the largest developing country in the world, the regional inequality is still a major obstacle to the equitable development of higher education in China. With the 1270 higher education institutions listed by the Chinese Ministry of Education in 2021 as the research objects, the degree of regional inequality of higher education development (HED), and its influencing factors, was visualized after being calculated by geo-statistical methods, such as geographical detectors. The results show that, first, HED in China shows regional linkage and hierarchical connection in high-value regions in the input and outcome dimensions. Second, the input dimension is still the leading factor restricting current HED in China. At the local scale, the geographical stratification characteristics of the four dimensions are evident. The restriction of the educational process covers a wide range and is concentrated in areas with the high-value regions of HED. The innovation of the research is the analysis of the geographical stratification of mechanisms, which identifies regional differences in the factors affecting HED in China.