The era of digital economy provides new means of value creation and value distribution for medical insurance governance. The unlimited nature of data information, the innovativeness of algorithm processing, and the networking supported by computing power makes the new pattern of medical insurance governance of joint construction, joint governance, and sharing a reality. This article uses the integrated analysis framework of “subject-resource-content” and emphasizes the integration and sharing of governance subjects and governance resources from the six dimensions of top-level design, management mechanism, service mechanism, delivery mechanism, supervision mechanism and consultation mechanism. It clarifies the governance contents such as the improvement of the medical insurance system, the optimization of medical insurance management, the balance between supply and demand of medical insurance services, and the expansion of medical insurance application scenarios. While the digital economy brings digital dividends to medical insurance governance, it also presents problems such as limited scalability of digital innovation, fragility of the medical insurance governance system, and structural imbalances in the service supply. Accordingly, this article believes that promoting the mechanism innovation of medical insurance governance through integrated management of medical insurance business, integration of medical insurance service platforms, intelligent application of medical insurance products, digital supervision of medical insurance funds, and network linkage of medical insurance entities, which can help to achieve structured integration and dynamic application of medical insurance joint governance. At the same time, policy optimization of medical insurance governance in the digital economy era can be achieved from aspects such as digital health-embedded service scenarios, digital dividend-empowered system efficiency, digital wisdom boosting management, and digital legislation leading policies and supervisions.