Improving fiscal health expenditure efficiency is an inherent requirement of the strategy of “healthy China” and “high-quality development”. The outbreak of COVID-19 has highlighted the importance of efficient health system. First, this paper systematically sorts out the multiple theoretical mechanisms of the positive and negative relationship between vertical fiscal imbalance and fiscal health expenditure efficiency. Secondly, a comprehensive index system, including the quantity and quality of medical services, is constructed, and the super-efficiency DEA model is used to measure fiscal health expenditure efficiency. There are obvious differences between eastern and western regions. Finally, the fixed effect model is constructed to carry out empirical research and it is found that the vertical fiscal imbalance in China has an overall positive and significant impact on the fiscal health expenditure efficiency, which is mainly achieved by optimizing the resources allocation between primary medical institutions and hospitals. Heterogeneity analysis shows that transfer payment scale has a corrective effect on the vertical fiscal imbalance’s effect. The result of quantile regression shows that the impact of vertical fiscal imbalance is not constant, and it gradually turns from positive to negative along with the improvement of fiscal health expenditure efficiency.