Science City which relies on large-scale scientific facilities is one of the main carriers of original innovation, and is of great significance for China to become a powerful country in science and technology in the world. Based on the existing research, the analysis framework of innovation ecosystem of Science City was constructed from the perspective of structuralism, and taks Huairou Science City in Beijing as an example to analyzes the integrity and internal and external synchronicity of the innovation ecosystem. From the perspective of integrity, the innovation subject types of innovation ecosystem in Huairou Science City are relatively single, and population diversity of the innovative ecosystem is in lack.From the synchronic point of view, the knowledge and information interaction within the system and between the internal and external of the system is insufficient.In view of these problems, policy suggestions for further promoting the creation and evolution of innovation ecosystem in Huairou Science City were put forward from three aspects promoting a large number of innovative elements gathering and polymerization reaction, guiding the full cooperation and self-organization between the innovation subjects and creating an open and innovative environment suitable for research, business and living.