Improving the scale and effectiveness of China’s energy conservation and environmental protection fiscal expenditure is crucial to enhancing the capacity of ecological and environmental governance of China, considering the dual perspectives of pollution governance and public health. This article first explains the mechanism by which national energy conservation and environmental protection fiscal expenditure can improve pollution control and promote public health. Secondly, this article scrutinizes the current status and limitations of China’s fiscal expenditure, highlighting the contribution of fiscal expenditure in the construction of ecological civilization from the standpoints of environmental governance and public health. Additionally, this study empirically uses DEA to measure the efficiency of the government’s fiscal expenditure. Conclusions found that: First, environmental protection fiscal expenditure is mainly focused on technological transformation and pollution control, while relatively little is spent on public health protection. Second, the efficiency of environmental protection fiscal funds is relatively low. These suggestions aim to optimize the positive impact of energy conservation and environmental protection fiscal expenditure for improving pollution governance and promoting public health.