Based on the construction of different caliber fiscal decentralization and local public health expenditure index, this paper makes an empirical analysis of the influencing factors of local public health expenditure in China by using the methods of FGLS and dynamic panel GMM. It is found that different fiscal decentralization indicators have different effects on public health expenditure, and local governments have a large right of financial autonomy to effectively increase public health expenditure, and the central government's transfer payment to local governments also has a significant positive effect on local public health expenditure. In addition, the difference in the level of local economic development will result in uneven local public health expenditure, manifested in the double imbalance between the expenditure structure and the provision of public health services. Therefore, China should continue to increase the central transfer payment, reasonably divide the central and local financial authority, establish a hard restraint mechanism of local public health expenditure, clarify the expenditure responsibility boundary between the central and local governments, and implement the measures of combining central supervision and control with local financial autonomy, in order to solve the problem of the double imbalance between regional and regional expenditure of local public health expenditure and ensure the effective supply of local public health products.