In the international community after the COVID-19 epidemic, the changes in the world are not only reflected in the macro-level of national politics and economy, but also reflected in the micro-level with public security awareness and measures. In China??s contemporary urban system, large-scale commercial complexes occupy the central area of the city as public indoor areas with a dense flow of pedestrian. During the epidemic, commercial complexes must realize the fastest and most effective protection function when dealing with emergencies. Based on the quantitative experimental data provided by the SEIR pathology model in terms of virus transmission and infection rate in different periods, the world has put forward more and more specific and strict requirements for epidemic prevention. This paper uses Matlab to form different units of large-scale commercial complexes into different units in the virtual experience space, and conduct experiments on the changes in the flow of pedestrian and the density of pedestrian in different time periods and different types of businesses as different targets. At the same time, the data visualization in virtual reality and simulation analysis are carried out, and the adjustment strategy of the space design protection is proposed accordingly. This paper discusses how to design the flow line of pedestrian in the public commercial space with medium and high density population to reduce the impact of emergencies.