China has formed a national emergency management system consisting of “one contingency plan and three sets of institutions” since the outbreak of the severe acute respiratory syndrome (SARS) in 2003. This system is further improved after the establishment of the Ministry of Emergency Management in 2018 and the great achievements made in the fight against the coronavirus disease 2019 (COVID-19). This study aims to improve China’s public health emergency command system via investigating the history, current status, and challenges of the system. In this article, we summarize the emergency command systems responding to the SARS outbreak, the H1N1 2009 pandemic, and the COVID-19 pandemic using literature research, theoretical analysis, and case comparison. China’s public health emergency command system played a significant role in dealing with these public health emergencies and has been increasingly improved; however, it still faces various challenges. Therefore, we propose several policy suggestions to address these challenges, which involve the aspects of joint prevention and control mechanism, system of law for public health emergencies, advisory board, and central–local relations.