Based on the panel data of 30 provinces and cities in China from the year 2008 to 2017, this paper uses the panel regression model to explore the direct impact of the I nternet on regional innovation capabilities, and on this basis, the mediating effect of the innovation factors flow is examined. The empirical study results show that, on the one hand, the Internet directly promotes the enhancement of regional innovation capabilities, and its promotion effect on the eastern and central regions is significantly greater than that of the western regions. On the other hand, the Internet has affected regional innovation capabilities indirectly by affecting the innovation factors flow. However, the impact of the innovation factors flow in different regions is significantly different. In the eastern and central regions, the Internet has further enhanced regional innovation capabilities by promoting the flow of innovation elements, while in the western region, the Internet has a negative impact on the flow of innovation factors, resulting in a decline in the region’s innovation capabilities.