Metagenomics is a tool of novel genomic methods to accurately study the composition of microbial communities in their ecological environment and is used in many fields, including mass transport systems. However, the pathogenic microbiomes found in these built environments have not been studied, although these areas represent a potentially important point of exposure. In this study, we used high-throughput sequencing to identify microbiota sampled from the Metropolitan Transport of Shanghai (MTS) in spring and summer. The metagenomic approach and analysis of influencing factors were used to capture a broad spectrum of microbiota, particularly pathogens, and models for mapping diversity and environmental factors. The results illustrate that among all 108 aerosol samples in spring and summer sequenced, bacteria accounted for 95.26% of the classified genes, while the remaining 4.73% were from eukaryotes, viruses, and archaea. We uncovered 86 pathogens matched with the List of Pathogenic Microorganisms of Human Transmission. Temperature, humidity, season and times of day do have significant effects on microbiota distribution and diversity. The results of this research provide a comprehensive and unbiased perspective on the characteristics of microbial communities and pathogens in urban metros, establishing a framework for exploring and assessing potential public health risks and providing early warning of biosecurity associated with these built environments. This study of pathogenic microbiomes in aerosol samples will be of interest to environmental and public health researchers.