Based on the analysis of hierarchical structure theory, it is concluded that the internal main body of science and technology finance has typical hierarchical structure characteristics. By constructing a Two-level hierarchical linear model, this paper makes an empirical analysis of the scientific and technological innovation output of the ecological role of science and technology finance in Shanghai, and compares eight models that do not consider hierarchical function and hierarchical function. The results show that Shanghai's science and technology finance ecology passes through. The cross-level interaction with the internal subject of science and technology finance influences the output of science and technology innovation, and shows the trend of increasing returns to scale; the economic environment, policy environment and institutional environment which constitute the ecology of science and technology finance interact with each other and act on science and technology innovation together; the influence of various environmental factors on the internal subject of science and technology finance is different. In the future, we should optimize the ecological construction of science, technology and finance in Shanghai from the perspective of hierarchical structure.