Although it is clear that respiratory pathogens are transmitted through droplets and physical contact in Fangcang shelter hospitals (FSHs), the potential for long-range transmission is poorly understood (Offord, 2020; WHO, 2020), and the effective ventilation rate for epidemic prevention in large public spaces is also not yet known. We investigated the pathogen-laden aerosol aerodynamics for the first time in the FSH using a model bacteria indication of the pathogen, concurrently examining ventilation rates on their long-range transmission. The study found that aerosols with sizes smaller than 3.3 μm could facilitate the long-range transmission of pathogens. Poor ventilation results in an increase in contamination levels, but excessive ventilation (12 ACH) may trigger a diminishing return phenomenon of ventilation within the FSH, and worsen aerosol deposition. For this FSH, an ideal ventilation rate was close to 10 ACH, and pathogen-laden aerosols were reduced by 29.54% and 26.77% in the pollution zone and surveyed patient shelter block (PSB), respectively, compared to the design values. Our study contributes to cleaner production in the FSH, as well as to the sustainability of healthcare services and the environment. Some of the findings can be generalized to some extent for similar large public spaces.