The outbreak of major health emergencies, such as the COVID-19 pandemic, has posed numerous challenges to waste management. Environmentally sound treatment of such epidemic-related municipal solid waste (MSW) plays a vital role in interrupting virus transmission. In this study, the furnace type, incineration process and control parameters of an MSW incinerator were comparatively analyzed with those of a medical waste incinerator and hazardous waste incinerator according to China’s MSW incineration pollution control standards. In addition, changes in flue gas emissions data before, during and after the outbreak of the pandemic were empirically analyzed. The study revealed the following: (1) the feasibility of MSW incinerators to meet the harmless disposal of potentially viral municipal solid waste (PVMSW); (2) the priority order of incinerator types for MSW incinerators in the disposal of potentially virulent waste was grate furnace incinerator > fluidized bed incinerator > cement kiln; and (3) when MSW incinerators treated PVMSW, the emissions of dioxin compounds in the flue gas fluctuated between 0.00052 and 0.031 ng TEQ/m3, HCl emissions fluctuated between 1.6 and 23.742 mg/m3, CO emissions fluctuated between 0.18 and 59.15 mg/m3, heavy metal emissions fluctuated between 0.000008 and 0.855 mg/m3, and particulate matter emissions fluctuated between 0.64 and 12.13 mg/m3. All emissions met the flue gas emission standards. This study verified the feasibility of using MSW incinerators to treat PVMSW during a sudden major pandemic and provided a theoretical basis for the environmentally sound collaborative treatment of PVMSW and a reference for the emergency management and sustainable development of MSW.