Emergency management of municipal solid waste during public health emergencies is crucial for curbing the spread of viruses and controlling environmental pollution. Most existing solid waste management systems, are designed with a top-down approach, covering multiple industries and sectors. However, these systems often fail to effectively manage potentially viral solid waste in household waste, which impedes effective solid waste management during public health emergencies and increases the risk of viral outbreaks. For example, during the COVID-19 outbreak, negligent management of potentially viral solid waste may result in the formation of a potential transmission chain of COVID-19 virus. Improper waste management may contaminate natural vectors such as water, soil and air, thereby increasing the pathways of human contact with infected vectors and promoting the risk of transmission of viral diseases such as dengue, Zika and hepatitis A. In this study, the applicability and limitations of the Chinese public emergency management system in the disposal of Potentially Viral/Viral Municipal Solid Waste (PVMSW) were analyzed in the breakout of public health crises. To address the need for precise risk control, efficient collaboration among key stakeholders, functional integration crossing multiple management organizations and flexible responses to complex situations, we proposed a PVMSW emergency management system based on a "Beam-Column Structure" model. This system consists of four modules: main traction, organizational leadership, functional articulation and demand matching. Each module is supported by the corresponding safeguards, including multi-level subject responsibilities, multi-scenario organization and implementation, multi-chain process connection and multi-demand control methods. The PVMSW emergency management system proposed in this study contributes to extending the framework of existing waste management protocols and enhancing the timely collection, transportation and disposal of PVMSW in public health crises. It offers valuable insights and guidance on the practices for improving risk awareness and management capacity in China's solid waste emergency response.