In order to study the development trend of the Internet’s role in supporting enterprise innovation, a new method based on deep learning algorithm and knowledge graph technology is proposed. Experiments show that the accuracy, F1 value, recall rate and precision of the algorithm are distinctly improved compared with the existing algorithms. A new algorithm is applied to analyze the innovation evolution of Chinese enterprises, using papers, patents and other documents between 1905 and 2020 as data sources. Based on the experimental results, the development stages can be divided into five stages. The research focus is on product R&D innovation, manufacturing innovation, marketing innovation, resource allocation innovation and organizational innovation. It can be seen that the development process of the Internet supporting enterprise innovation system is an evolutionary development process from point to line, to surface, to the body, and to the ecosystem.