China has made significant progress in modernizing its healthcare system in the past 20 years. However, there are some issues that are difficult to solve on the current healthcare status, including the lack of medical care satisfaction in rural areas and urban areas, excessive consumption of medical resources, conflict and tension between the healthcare provider and patients, and the problems caused by the change of model of healthcare. Therefore, the State Council in-troduced the Opinions of the CPC Central Committee and the State Council on Deepening the Health Care System Reform in 2009 in order to provide basic, safe, effective, convenient and affordable healthcare for all residents. Despite the goals and policies set by the gov-ernment, how to implement them remains to be chal-lenging. Like evidence-based medicine, comparative effective research ( CER ) which started in the US in 2000 ’s can provide diagnosis and treatment information for patients, doctors, and health policy makers to make decisions on the effective ways of caring for both indi-vidual and population. It also may apply to the condi-tions of healthcare reform in China. And there are op-portunities and challenges of conducting CER in our country. We suggest that the government should estab-lish the national-level CER research institute, CER Leadership Committee and relevant standards, fund the CER projects, and begin CER in certain disciplines.