Promoting industrial structure upgrade, upgrading industrial structure and solving the contradictions existing in industrial structure are the key concerns of economic development in this era. Based on this, this paper takes 30 provinces, municipalities directly under the central government and autonomous regions of China from 2009 to 2019 as research samples to study the influence of innovation capacity on industrial structure. The research results show that the influence of innovation capacity on industrial structure is in an inverted "U" shape, and the current innovation development is in the stage of inhibiting the development of industrial structure, but with the continuous improvement of innovation capacity, the subsequent development of industrial structure will be promoted. The size of the government and the economy of developed regions have a positive effect on the development of industrial structure, while the increase of urbanization level has an inhibiting effect on the development of industrial structure. Therefore, each region should continuously increase innovation investment and promote the combination of industry, academia and research, so as to promote the upgrading and development of industrial structure.