The past COVID-19 pandemic introduced the world to the necessity of dealing with the trade-off between minimizing probability of contagion, and providing people with services they need. This trade-off stipulates that a large person-to-person distance will reduce contagion probability, but will render service inefficient, and vice versa. This work focuses on the urban rail transit (URT) hub, as an example of a busy passenger area, from which we can derive an optimal preparedness policy to use during the pandemic time of any coronaviruses. We use simulation methodology, based on the classical social force model, to represent behaviors and characteristics of pedestrians. Passenger flow movement process is a mechanism we explore to figure out how the epidemic management policy and pedestrian psychological-related behaviors interact with the URT system. The systems’ complexity regarding contagion-prevention distances are tested over a few scenarios: before/after the outbreak, and for different person-to-person distances demonstrating different crowd levels. A case study of Xinjiekou Station, Nanjing URT, China, enables assessment of passenger management policy with person-to-person distances of 0.5 m, 1.0 m and 2.0 m. Multi-scenario performance illustrates the trade-off in dynamic between the efficiency of pedestrians’ walking behaviors and the distancing needs for preventing coronaviruses transmission. The results show that queuing length with social distancing of 1.0 m and 2.0 m is increased by 4.17% and 21.22%. The average delays in boarding are 14.1 s and 22.5 s for 1.0 m and 2.0 m, which leads to 15.29% and 22.39% increases, respectively, in comparison with ordinary social distancing of about 0.5 m.