Abstract: Taking "City Brain" as the infrastructure and underlying support for urban operation and governance is the major trend in the future. The successful construction of "City Brain" cannot be achieved without the benign mutual promotion mechanism of government and enterprise. Based on the survey of the "City Brain" construction subjects in Haidian District, Beijing, an embedded case method was used to analyze the complementary relationship, structural logic, and mechanism of government-enterprise innovation partnership mechanism. The research finds that: (1) in the government-enterprise innovation partnership mechanism , the government and enterprises have established a long-term healthy complementary relationship; (2) the partnership mechanism of government-enterprise innovation is an organic combination of "government coordination + system guarantee + market operation". Government behavior shifts to public service functions and overall planning, generating scarce institutional resources, and determining the direction and quality of the "City Brain" through top users; micro enterprises respond to the needs of government user in a market-oriented competitive environment that is compatible with innovation incentives, and influence the direction and quality of government demand through the feedback mechanism. The government-enterprise innovation partnership mechanism has formed an organic combination of limited public service-oriented government and competitive markets, which provides an empirical basis for handling the relationship between government and enterprises.