In the process of medical resource scheduling, it is difficult to ensure the comprehensive utilization rate of the corresponding resources due to the influence of the correlation between digital medical resource data. Therefore, research on digital medical resource scheduling method considering data interoperability is proposed. After realizing the representation of data and its processing process in digital medical data warehouse with the help of metadata, two ways of direct conversion and indirect conversion are adopted respectively, and an interoperability mechanism in the form of XML document is constructed for the original metadata stream of digital medical resources. In the specific scheduling process, according to the task status between the target node and the digital center, the digital medical resource scheduling center is determined, and the resource scheduling is realized by combining the promotion of different digital medical resource data to the main task operation ability. In the test results, the influence of increasing the number of task requests on the comprehensive utilization rate of resources is not obvious, and it is always stable in the range of 0.85-0.92.