Exploring the influence and mechanism of the development of higher education on the upgrading of manufacturing structure is helpful to promote the process of the upgrading of manufacturing structure in China. Based on the inter provincial panel data of 27 provinces (cities and autonomous regions) in China from 2008 to 2017, this paper explores the impact and mechanism of education of higher learning development on the upgrading of manufacturing structure by constructing fixed effect model and intermediary effect model. The research shows that education of higher learning can promote the optimization and upgrading of Chinas manufacturing industry structure through two ways: improving the accumulation of human capital and promoting technological innovation. The industrial heterogeneity test shows that the development of education of higher learning has a significant positive correlation with labor intensive manufacturing industry and a significant negative correlation with technology intensive manufacturing industry. The regional heterogeneity analysis shows that the development of education of higher learning in central China has a significant positive impact on the structural optimization and upgrading of manufacturing industry. Based on the empirical results, it can be seen that increasing the investment in higher education, rationally allocating education of higher learning resources among regions and optimizing the discipline and specialty setting of talent cultivation are crucial to the upgrading of Chinas manufacturing structure.