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Bioaerosols are widely distributed in urban air and can be transmitted across the atmosphere, biosphere, and anthroposphere, resulting in infectious diseases. Automobile air conditioning (AAC) filters can trap airborne microbes. In this study, AAC filters were used to investigate the abundance and pathogenicity of airborne microorganisms in typical Chinese and European cities. Culturable bacteria and fungi concentrations were determined using microbial culturing. High-throughput sequencing was employed to analyze microbial community structures. The levels of culturable bioaerosols in Chinese and European cities exhibited disparities (Analysis of Variance, P < 0.01). The most dominant pathogenic bacteria and fungi were similar in Chinese (Mycobacterium : 18.2–18.9 %; Cladosporium : 23.0–30.2 %) and European cities (Mycobacterium : 15.4–37.7 %; Cladosporium : 18.1–29.3 %). Bartonella , Bordetella , Alternaria, and Aspergillus were also widely identified. BugBase analysis showed that microbiomes in China exhibited higher abundances of mobile genetic elements (MGEs) and biofilm formation capacity than those in Europe, indicating higher health risks. Through co-occurrence network analysis, heavy metals such as zinc were found to correlate with microorganism abundance; most bacteria were inversely associated, while fungi exhibited greater tolerance, indicating that heavy metals affect the growth and reproduction of bioaerosol microorganisms. This study elucidates the influence of social and environmental factors on shaping microbial community structures, offering practical insights for preventing and controlling regional bioaerosol pollution. [Display omitted] • Chinese urban had higher levels of culturable bioaerosol pollution than Europe. • Pathogens Mycobacterium and Cladosporium were highly prevalent in China and Europe. • Bacteria in China showed higher MGEs abundance and biofilm-forming capacity. • Environment and socio-economic factors shaped microbial community structure. • Heavy metals widely present in ACC influence microbial growth and reproduction. [ABSTRACT FROM AUTHOR]