Objective: To establish the whole life cycle tracking audit system of public hospital information system, avoid the risk of high investment and low efficiency of information system, and improve the sustainability of hospital operation. Methods: From the perspective of the whole life cycle of the information system, it is closely combined with the characteristics of the public hospital information system and the audit objectives. With the help of the information technology business management system model, it takes business audit evaluation as the basis and takes technical audit evaluation as the means, and then controls through management audit evaluation. Re- sult: An information system tracking audit evaluation system is built, consisting of 4 first level indicators, 18 second level indicators, and 77 third level indicators. Conclusion: It is needed to ensure that the construction of public hospital information system is moder- ately advanced and optimal at this stage, so as to provide reference for the follow-up audit of public hospital information system.