With the continuous reform of China’s medical system, people’s health needs are also rising, so people have higher requirements for public medical services. At present, the economic business activities and asset management of public hospitals are becoming increasingly complicated, and the pressure of operation management is increasing. It has promoted the hospital to optimize the allocation of resource allocation and improve the operating efficiency. The management model has changed from extensive to refined, promoting the sustainable development of public hospitals. This article first starts with the development status and significance of the construction of the internal control system of the public hospital, and then sorts out the internal control of existing problems in the public hospital. The article proposes the content and efforts of the construction of an internal control system for existing problems. In the process, ideas for improvement were proposed. It is hoped that through the improvement of the management level of the hospital’s internal control system, in a changing market environment, it will better meet the needs of patients and contribute to the healthy and sustainable development of medical institutions.