Abstract Based on the balanced panel data of 30 provinces from 2000 to 2018, this paper examines the intermediary mechanism of human capital misallocation that affects industrial structure. The results show that human capital misallocation has a negative impact on industrial structure upgrading. The further test results of intermediary effect indicate that human capital misallocation not only inhibits technological innovation and leads to deviation of industrial structure, but also restricts income growth of competitive sectors, widens the income gap between the two sectors and hinders the upgrading of industrial structure. The are some intermediary effects in the model which account for 17.93%, 14.54%, 15.16% and 19.73% respectively. Further sub-regional regression results also show that the distortion effect and mediation effect in the eastern region are smaller, while the distortion effect and mediation effect in the central and western regions are larger. Therefore, correcting the mismatch of human capital and realizing the correct allocation of human capital between monopoly departments and competitive departments is helpful for enterprises to promote the upgrading of industrial structure and realize high-quality development.