In order to improve public health by more effectively curbing the prevalence of chronic non-communicable diseases, the Chinese Academy of Engineering organized a major advisory project in 2015: the Strategic Study on the Health Economics Applied to Policymaking for the Prevention and Control of Chronic Non-Communicable Diseases. The study demonstrated health economics to be an important decision-making tool that may be applied to the prevention and control of chronic non-communicable diseases while they remain at a primary stage. However, a lack of understanding of the importance of health economics application and limitations in mastering and using the methods of health economics restrict the application of this tool in policymaking for the prevention and control of chronic non-communicable diseases. We suggest that multi-subject participation in health economics studies should be improved in future, big data related to health economics should be accumulated and applied to policymaking for the prevention and control of chronic non-communicable diseases, and the strategic framework of health economics should be developed and applied to policymaking for the prevention and control of chronic non-communicable diseases.