Considering the impact of science and technology resource allocation on regional innovation output, based on the inter-provincial panel data of 30 provinces in China from 1998 to 2017, this paper establishes a regional innovation output growth model, including science and technology resource input and science and technology resource allocation, and investigates the spatial relationship between regional innovation output and the allocation of science and technology resources, the effect of the inter-subjective configuration structure and inter-regional space re-allocation on regional innovation output. The research results show that there are obvious spatial autocorrelation agglomeration characteristics of China’s regional innovation output and science and technology resource input. The efficiency of the allocation of science and technology resources in the region is relatively low. The application-oriented research subjects with enterprise-oriented research are more efficient in investing in science and technology resources, and the promotion of regional innovation output is more significant. The investment in science and technology resources in neighboring provinces will have a significant inhibitory effect on the province’s innovation output. The regional mobility of science and technology resources has a significant role in promoting regional innovation output growth. The effect of science and technology personnel mobility on regional innovation output is better than that of technology capital flows.

Population mobility and the expansion of construction land in industrial development promote urbanization, and the sustainable development of cities creates requirements for the green transformation of industry. This paper uses the directional distance function (DDF) and the global Malmquist–Luenberger (GML) index method—including urbanization factors—to calculate the industrial green transformation (IGT) index in China, and to analyze its evolution and spatial distribution characteristics. The results show that ignoring the urbanization factor will lead to the overestimation of the IGT. The growth of the index has multiple stages, and it shows a decreasing order in the middle, east and west regions. Overall, the distribution of the index spreads out over time, and the gap widens. In terms of spatial correlation, high values are mostly concentrated in the eastern region and low values are mostly concentrated in the western region, and the gap in the eastern region is larger than those in the central and western regions. Therefore, in addition to the transformation of industrial production into a circular economy model, it is also necessary to promote the circulation of technical talent between regions in the development of urbanization, reducing the unbalanced development between regions and comprehensively promoting the green transformation of industry.