To promote the standardization of hospital informatization construction work, strengthen the construction of hospital information management, supervision, guidance and assessment, this paper constructs a hospital information system evaluation system model with a broad representativeness, which makes the process of hospital information can be sustained and healthy developed. It calculates every single index weight by using the Analytic Hierarchy Process method, so that it can get the total score of the system performance testing and functional testing. With the score it can make the comprehensive evaluation of hospital information system. It scientifically evaluates the information system of two Affiliated Hospital of Xinjiang Medical University by the model, and gives the suggestions to improve the work.