As the pace of hospital informatization construction continues to accelerate, information network technologies are being used more and more extensively in the medical industry. These advanced technologies make medical businesses more and more dependent on industry information and data, which brings about network system security issues that cannot be ignored. To strengthen the daily operation and management of hospitals, ensure the stable operation of computer systems, and do a good job in protecting the security of hospital computer system network information, this paper designs a risk assessment method for hospital computer network information security based on SAE deep neural network and analyzes the main factors affecting the security of hospital computer system network information. The experimental results prove that the proposed method can effectively improve the reliability of the evaluation results and ensure the accuracy of the evaluation results. According to the obtained information security model, it can effectively guide the construction and application of hospital computer network information systems, optimize the system network, and promote the development of hospital informatization.