Scientific research is one of the main tasks of modern research hospitals. This paper analyzes the management of medical scientific research in China from three aspects: organizational structure, management system and work function. It is found that there are some problems in the management of medical clinical scientific research, such as lagging management system, unclear management orientation, low conversion and utilization rate of scientific research achievements, and low professional level of management team. In order to adapt to the actual needs of clinical scientific research, it is suggested to optimize the current management system and mode of medical clinical scientific research by changing the functions of scientific research management, improving the work of scientific research evaluation, promoting the transformation and utilization of achievements, paying attention to the training of talents and improving the quality of scientific research managers.