Taiwan's national health program system has been commenced in 1995, and it successfully reduces the gap in access and health among different income levels and groups. However, soon after its inauguration, the system encountered the balance problem of budget. Although the Government always wants to adjust the premium rates so as to increase the revenue to meet the fast growth of payments and to maintain the normal operation of the system, it is difficult to get consent from the public and legislative representatives because of some controversial issues, such as delayed payments by various branches of government, the drug price black hole, the controversy over high annual year-end bonuses for employees of Health Insurance Bureau, the waste of medical resources by some people, the growing incidence of fraud premium claims from some hospitals, and other political factors. In fact, many factors affect the accumulation of reserve fund of National Health Insurance, and they interact and influence each other to form a complex structure. In this study, we take a whole view and apply system dynamics to investigate the interaction and causality among factors that affect the balance of NHI reserve fund to increase the understanding of this complex behavior. The impacts of the second-generation health insurance policy, aging population and advances in medical technology on the NHI fund reserve are also discussed in this paper.