BACKGROUND The "National" Health Insurance (NHI) in Taiwan, China is a single-payer system that was introduced in 1995 to provide universal health care. It is worth noting that three stakeholders are involved in Taiwan's NHI, which can be seen as a triangular governance regime between the Bureau of "National" Health Insurance (BNHI), the insured and providers. Accordingly, this study intended to assess the efficiency of various different production processes that occur among these stakeholders in Taiwan's NHI system. METHODS A two-stage relational Data Envelopment Analysis (DEA) model is adopted to investigate the sub-process efficiencies of the health care resources held by 23 cities and counties through stages I or II, where the outputs of the first stage serve the inputs of the second. The dataset was collected from the annual reports published by the Department of Health, Taiwan, China. RESULTS Under the proposed framework, the efficiency of the whole process can be obtained from the product of productivity and allocative efficiency. Ten DMUs are efficient either in stages I or II, with only two DMUs being efficient with regard to both sub-processes. CONCLUSIONS The relational DEA model not only demonstrates the physical relationship between the whole process and the sub-process components, but also produces reliable outcomes in efficiency measurement among different stakeholders in Taiwan's NHI system.