This study takes the National Disease Prevention and Control Agency of China (NDCPA) and the European Center for Disease Prevention and Control (ECDC) as representatives to compare the reform paths of disease control agencies after Covid-19 under China and Europe context. By drawing on existing analytical framework and analyzing the content of the laws, regulations and official documents of the two agencies, this paper systematically evaluates them in terms of the three dimensions: institutional independence, social accountability, and scope of responsibilities. The results show that compared with ECDC as an independent agency, NDCPA still has a huge gap in terms of institutional independence and social accountability, yet its responsibilities are more comprehensive. Superficially, the establishment of the NDCPA has enhanced the strength and administrative status in China’s public health crisis governance system, but it is essentially a consolidation of the previous structure under the domination of the administrative force, and its professionalism is still subject to the government at all levels and lacks a clear guarantee at the legal level. ECDC’s authority has grown during the past transboundary public health crises, and its role has gradually increased from technical support to policy coordinator, but its power mainly relies on the EU mandate to cooperate with member states, and their professional advice lacks coercive force, requiring greater commitment from member states to achieve more cohesive and effective transboundary health governance.