Bioaerosols are more likely to accumulate in the residential environment, and long-term inhalation may lead to a variety of diseases and allergies. Here, we studied the distribution, influencing factors and diffusion characteristics of indoor and outdoor microbiota pollution in six residential buildings in Guangzhou, southern China over a period of one year. The results showed that the particle sizes of bioaerosol were mainly in the range of inhalable particle size (<4.7 μm) with a small difference among four seasons (74.61 % ± 2.17 %). The microbial communities showed obvious seasonal differences with high abundance in summer, but no obvious geographical differences. Among them, the bacteria were more abundant than the fungi. The dominant microbes in indoor and outdoor environments were similar, with Anoxybacillu, Brevibacillus and Acinetobacter as the dominant bacteria, and Cladosporium, Penicillium and Alternaria as the dominant fungi. The airborne microbiomes were more sensitive to temperature and particulate matter (PM2.5, PM10) concentrations. Based on the Sloan neutral model, bacteria were more prone to random diffusion than fungi, and the airborne microbiome can be randomly distributed in indoor and outdoor environments and between the two environments in each season. Bioaerosol in indoor was mainly from outdoor. The health risk evaluation showed that the indoor inhalation risks were higher than those outdoor. The air purifier had a better removal efficiency on 1.1–4.7 μm microorganisms, and the removal efficiency on Gram-negative bacteria was better than that on Gram-positive bacteria. This study is of great significance for the risk assessment and control of residential indoor bioaerosol exposure.