Developing higher education is a positive measure to deal with the aging population and drive the upgrading of industrial structure. Based on the empirical analysis of China’s inter provincial panel data from 2009 to 2018, it is found that the aging population hinders the upgrading of China’s current industrial structure. The adjustment effect analysis shows that the increase of investment in higher education helps to weaken the negative impact of population aging on the upgrading of industrial structure. The mechanism test shows that the promotion effect of the increase in higher educational investment on the upgrading of industrial structure is mainly based on the intermediary mechanism of the advancement of human capital. The intermediary mechanism based on scientific and technological output has no significant effect, which shows that the supply of scientific and technological output in colleges and universities can not effectively match the demand for science and technology caused by the upgrading of industrial structure.