Membrane bioreactors (MBRs) have become one of the most promising technologies in wastewater treatment. This study aimed to investigate the emission characteristics, source analysis and health risk of bioaerosols generated from a wastewater treatment plant (WWTP) with an MBR throughout the entire process. The results suggested that the MBR exhibited a high concentration of bacterial bioaerosols (2921–6173 CFU/m3) and fungal bioaerosols (77–673 CFU/m3) and a high proportion of the respiratory fraction (RF) of bioaerosols. In the MBR, Halomonas, Microvirga, and Geodermatophilus and Rubellimicrobium were the dominant bacteria, and the predominant fungi were Acidea, Neophaeosphaeria, and Cryptotrichosporon. Water soluble ions (WSIs) in the bioaerosols were mainly SO42-, NO3-, Cl-, Ca2+, Na+ and NH4+, with concentrations ranging from 18.68 to 183.41 μg/m3. Temperature, relative humidity (RH) and wind speed (WS) all had different influences on bacterial bioaerosols and fungal bioaerosols. Air was the major source of bioaerosols from the MBR. Bioaerosols in the fine grid (FG) and sludge dewatering room (SDR) were from wastewater, sludge and air. Furthermore, inhalation was the greatest pathway of bioaerosol exposure. The SDR, aeration tank (AerT) and MBR showed the highest risks of bioaerosols. Thus, bioaerosols from MBRs should be sufficiently investigated, and effective controls should be set up to protect workers and residents around plants.