Bioaerosols are one of the main types of aerosols originating from the Earth’s biosphere and are widely found in the atmosphere. They possess both biological attributes and aerosol characteristics, thereby have significant impacts on climate, the environment, ecosystems, and public health. However, their large-scale distribution, influencing factors, climatic and environmental effects remain unclear due to the scarcity of observational data. Our research team provides an integrated bioaerosol dataset based on a large-scale field campaign conducted across 45 stations in East Asia. It uses unified sampling and analytical methods in sites across China, Japan, South Korea, and Mongolia. The dataset integrates atmospheric bioaerosol number concentrations, bacterial community structure, related meteorological variables, air quality parameters and underlying surface types etc. Bioaerosol concentrations and microbial community data were obtained by fluorescence microscopy analysis and 16S rRNA gene sequencing. Further analysis of this integrated dataset shows that bioaerosol number concentrations are negatively correlated with local NDVI, and exhibit a clear relationship with air temperature with a peak at approximately 20 °C. It is a unique dataset of high value to the community and high potential reusability. This in-situ dataset provides a foundation for advancing research on atmospheric bioaerosol processes, as well as their implications for climate, environment, and interdisciplinary studies.