China’s higher education is rapidly developing, however, the phenomena such as the imbalance of regional development, unfairness of resources allocation and so on become more and more prominent. China’s higher education comprehensive development index is built through four dimensions of the entropy method from the scale of education, funds input, infrastructure and teachers to implement the global spatial autocorrelation analysis, local spatial autocorrelation analysis and the three-dimensional trend analysis for higher education in China. The results show that the level of higher education in China shows significant spatial positive correlation in general, and the spatial correlation gradually increases. However, the spatial heterogeneity of higher education in China is obvious through the analysis of local spatial autocorrelation. Backward areas still account for a large proportion, and the gap between the backward areas and the developed areas of higher education development is gradually expanding. Thus, the developed areas of China’s higher education do not effectively play a role in spatial radiation and driving, their spatial spillover effect is not obvious. The spatial structure of higher education development still needs to be improved. Chinese Government should avoid the expanding gap of regional difference of higher education, the less-developed areas should accelerate the development of higher education, the developed areas should effectively play a role in radiation and driving so that the spatial regional differentiation of higher education can be narrowed.