With the COVID-19 outbreak hitting the world, the frequency and severity of port congestion caused by various factors are increasing, challenging the stability of international supply chains. Thus, it is necessary to conduct an in-depth study on congestion risks to reduce their adverse impacts on congestion. Although traditional criticality analysis techniques may be capable of ranking port congestion risk in common scenarios, new risk analysis methods are urgently required to tackle uncertainty along with the COVID-19 pandemic. This paper develops a methodology designed for the identification and prioritization of port congestion risk during the pandemic. First, a novel congestion risk assessment model is established by extending the risk prioritization index (RPI) suggested by failure mode and effects analysis (FMEA). Next, the combination of fuzzy Bayesian reasoning, AHP and the variation coefficient method is incorporated into the model in a complementary way to facilitate the treatment of uncertainty and quantitative analysis of the congestion under the different influence of risk factors in ports. Finally, the mode introduces a set of risk utility values for calculating the RPI for prioritization. A real case study and a sensitivity analysis were carried out to illustrate and validate the proposed model. The results proved that the applied method is feasible and functional. In the illustrative example, the top three risk factors are “Interruption of railways/barges services”, “Skilled labor shortage” and “Shortage of truck-drivers/drayage truck”. The findings obtained from this paper could provide useful insights for risk prevention and mitigation.