Abstract: Technological innovation is the primary driving force for development, and implementing an innovation-driven development strategy is conducive to accelerating the transformation of new and old kinetic energy. But at this stage, China's technological innovation capability still has a lot of room for improvement. Studies have shown that the regional spatial structure has a significant impact on economic development, income levels and ecological environment. However, the existing literature seldom deals with the influence of regional spatial structure on regional innovation capability, and the internal influence mechanism of the two has not been deeply explored. Correctly identifying the impact of different types of spatial structures on scientific and technological innovation is an important way to promote the rational layout of regional spatial structures, and enhance the strength of regional scientific and technological innovation. Therefore, on the basis of theoretical analysis, this paper uses the panel data of 26 provinces and autonomous regions in the country from 2001 to 2018 to construct the regional spatial structure index, innovation efficiency index and innovation difference index. We examine the impact of regional spatial structure on innovation efficiency and innovation gap and its underlying mechanisms. On this basis, this paper further discusses the heterogeneity of the impact of regional spatial structure on technological innovation. The research results show that: (1) the single-center spatial structure is beneficial to the improvement of innovation efficiency, and it mainly functions through two mechanisms: agglomeration effect and scale effect; (2) The multi-center spatial structure is conducive to narrowing the innovation gap, and it mainly plays its role through three influencing mechanisms: the scale mutual loan effect, the industrial structure effect and the factor flow effect; (3) The single-center spatial structure is more suitable for provinces and cities in the efficiency-driven stage. For provinces and cities in the innovation-driven stage, the multi-center spatial structure is more conducive to innovation and high-quality development. The findings of this paper have several implications for the adjustment of China's provincial spatial structure and the development of scientific and technological innovation: First, clarify the important role of regional spatial structure in the development of scientific and technological innovation. The adjustment of regional spatial structure is one of the important means to promote the development of scientific and technological innovation. The Chinese government needs to clarify the functional positioning and interrelationships of cities within the province, rationally arrange the spatial structure within the province, and build a regional innovation chain with close cooperation. Second, promote the diversified development of regional spatial structure layout according to local conditions. Each province in China should adopt a reasonable spatial structure according to the actual situation of its own technological innovation and development. For example, while appropriately controlling the development scale of central cities, the eastern provinces should create a certain number of sub-central cities to promote the formation of a multi-center and multi-level spatial structure. For the central and western provinces, the improvement of innovation and development efficiency is the primary task. Therefore, the construction of central cities should be reasonably promoted to avoid blindly "spreading the pie" of development, resulting in waste of resources and low-level balanced development. Third, the development of scientific and technological innovation should not only focus on efficiency but also reflect fairness. China's existing science and technology innovation policies mainly focus on improving the overall efficiency of the innovation chain, but the large gap in science and technology innovation has gradually become one of the important problems that cannot be ignored. Therefore, while improving the efficiency of scientific and technological innovation resource allocation, the fairness of scientific and technological innovation should also be fully considered.