In terms of the medical information management system, it can effectively increase the resource utilization rate of medical and health institutions, optimize the management process, and provide relevant, efficient management approaches, all of which help medical and health institutions meet their internal and external demands to the greatest possible extent. However, the projects related to the information management system in hospitals or other medical institutions are characterized by high system complexity, multiple related links, and uncertainty of project demands due to their own professional and industrial characteristics, which are frequently manifested as many limiting factors in the construction process. It is essential to determine the kind of risk and evaluation methods to explore the risk evaluation indicators and formulate corresponding countermeasures for ongoing medical institution information systems projects. In such a background, this study establishes a perfect risk identification and evaluation system by taking the risk management of projects related to medical institution information system in R hospital as the research object and proposes the corresponding countermeasures as the reference for the establishment of the information management system.