COVID-19 epidemic has brought severe challenges to China's national governance system. As an important "epidemic" front in the fight against COVID-19 epidemic, online public opinion management aims at balancing the free expression of the public and risk control. In the new media era, COVID-19 epidemic has formed a complex public opinion field in cyberspace, which has increased the difficulty of government governance and exposed the governance defects of traditional social governance model. Comprehensive governance can effectively make up for the shortcomings of the traditional social governance model. Scientific prevention and accurate measures should be carried out from the three dimensions of governance concept, governance principles and methods and governance system. We will improve the governance efficiency of online public opinions on public health emergencies, form a new pattern of social governance on public health emergencies, and modernize the country's governance system and capacity.