At this stage, China is still an emerging market economy country, the market mechanism is not perfect, and the survival environment of Superconductor Magnetics Energy Storages is not optimistic. In order to enhance the market competitiveness of Superconductor Magnetics Energy Storage, governments at all levels increase their funding and policy support for their innovative research and development, which is of great significance to help them continue to develop. In this paper, panel data of 471 enterprises listed on shenzhen Small and Medium-sized board from 2014 to 2018 are selected, and regression model is used for empirical test to explore the impact of government funding policies on innovation and R&D of small and medium-sized enterprises.The results show that the government's funding policy has a positive effect on the R&D investment in science and technology as a whole, but has no direct impact on the output of innovative R&D.Only through investment in R & D personnel can it have a positive impact on innovative output. Therefore, government funding should focus on strengthening investment in scientific and technological personnel.