Medical overuse is the leading cause of high expenditure among healthcare systems worldwide, with the degree varying from region to region. There is increasing evidence to indicate that in China, National Healthcare Security Administration (NHSA) supervision plays the most crucial role in decreasing medical overuse. For medical overuse, traditional studies focus on empirical researches and qualitative analysis, most of which ignore how the two important participants, i.e., medical institutions and NHSA, affect the strategy of each other. To reduce the losses incurred by insufficient supervision, this study starts from bounded rationality, builds an evolutionary game model to study the relations between the NHSA and medical institutions, and reveals the dynamic evolution process of the supervision of NHSA and overuse of medical institutions. Through stable evolutionary strategy analysis, numerical simulation results, and sensitive experiments under diverse scenarios, we found that when profit gap of medical overuse is high or low, medical institution will adopt fixed strategy, which is medical overuse or appropriate medical use. Only when the profit gap is at a medium level will NHSA’s choice affects medical institutions’ strategy. Furthermore, NHSA’s strategy is affected by the profit gap between medical use and supervision cost. Our work enriches the understanding of supervision for medical overuse and provides theoretical support for the NHSA to make decisions to reach an ideal condition, i.e., to supervise without exertion.