Accumulating studies suggest that, as the subway is one of the important means of transport in cities, airborne microorganisms in its system have potential effects on human health, but previous studies have mainly focused on some foreign cities. We reviewed the spatio-temporal distribution characteristics of airborne microorganisms in subway stations in different cities, including diurnal, weekly, and seasonal variations, and the distribution of microorganisms in different regions of the world. The factors affecting airborne microorganisms, such as human activities, temperature and humidity, ventilation, and particulate matter, were presented. The potential health effects were described. Although there was no significant risk of infection from using subway, many pathogens do exist in the air. The influence of microorganisms in subway air on health has become a public health problem that cannot be ignored.