This paper proves that the development of the digital economy has become a new vector to promote the upgrading of China’s industrial structure. In addition, heterogeneous technological innovation plays an intermediary role in the promotion of the industrial structure by the digital economy. This study aims to solve the following: whether the development level of the digital economy is positively promoting the upgrading of the industrial structure; whether technological innovation can promote the upgrading of the industrial structure; the path of the digital economy through which to promote the upgrading of the industrial structure and the heterogeneity of this path. The purpose of this study was to verify the digital economy and scientific and technological innovation to promote the upgrading of the industrial structure and the reality of the realization path; and to solve the problem of insufficient power for upgrading China’s regional industrial structure against the background of the impact of the new generation of information technology. This study mainly adopted comprehensive evaluation and multivariate statistical analysis methods. The statistical basis for the study was data from 30 Chinese provinces from 2013 to 2018. The results confirm the hypothesis that the development of the digital economy and scientific and technological innovation have a positive role in promoting the upgrading of the industrial structure, and also prove that the intermediary role of heterogeneous technological innovation is crucial in the process of the digital economy promoting industrial upgrading. This conclusion can further give play to the role of the digital economy in promoting industrial structure upgrading, build a clean and intelligent industrial chain, solve the root cause of the lack of new drivers for China’s industrial upgrading, and help to form a new development pattern of domestic and international double circulation, so as to achieve the high-quality and sustainable development of China’s economy.