Globally, air pollution is intensifying in both urban and rural environments due to rapid urbanization and industrialization. It is widely accepted that human activities, particularly mining, contribute to increased concentrations of fine particulate matter in the atmosphere, leading to serious concerns regarding the associated health risks. In this study, the characteristics of outdoor aerosols containing bacteria and fungi were determined from on-site samples that were analyzed using sequencing techniques as well as modelling at both artificial and natural locations in two cities (Fuxin, FX; Guangzhou, GZ) in China. The interaction between urban and rural anthropogenic activities had a synergistic effect on the distribution of airborne microorganisms. At locations with artificial surfaces, which were characterized by higher population densities, the concentration of Firmicutes, including Streptococcus pneumoniae and Aspergillus fumigatus, which are colonizers of the human respiratory tract, was 1.25 times greater than that of the on-site monitored total airborne microbes (TAM) concentration. In the natural wetland area with a lower population density, the coarse-, medium-, and fine- bioaerosols accounted for 16%, 49%, and 35% of the TAM concentration, respectively. When a concentration ratio was used to describe the airborne bioaerosol (x: C/C′), the community distribution was found to vary between artificial and natural environments in FX. This was attributed to the contributions of agricultural and traffic activity. The accumulation and atmospheric diffusion of aerosols, particularly in areas with low wind speeds, led to the presence of inhalable (0.65‒2.1 μm) bioaerosols. Through a modeling-based analysis, elevated x values indicated a regional deterioration in air quality due to aerosol emissions and their spatial dispersion. This ratio was highlighted by the significant abundance of Ascomycota observed at transportation infrastructure sites in GZ. The study suggests the existence of health risks associated with regional atmospheric bioaerosols, with the risks varying across the urban-rural divide.