Aeration tanks in municipal wastewater treatment plants (WWTPs) are regarded as sources of bioaerosols, often containing particles and microbes. In this study, intestinal bacteria were investigated from biochemical reaction tanks (BRTs) of six municipal WWTPs. It was observed that 86 CFU/m3 of intestinal bacteria (in average) occurred in the BRTs installed surface aerator, which was higher than those adopted submerged aeration (67 CFU/m3 in average). 62.72% of fine particles were observed in the BRTs supplied oxygen by submerged aerator, while 75.73% of coarse particles emitted during surface aeration. Pseudomonas sp., Serratia sp. and Acinetobacter sp. were identified as pathogenic bacteria presented in the intestinal bacteria population and most of them existed initially in water or sludge, particularly in water surface. The emission level and particle size distribution were significantly correlated with aeration mode adopted by the WWTPs. The bioaerosols particles emitted from surface aeration process was higher than that from submerged aeration process. Meanwhile, the BRTs with submerged aerators released more fine particles, which can get into the alveoli and represented the potential challenge to human health. Canonical correspondence analysis results exhibited that population of intestinal bacteria had a positive correlation with aeration rate and water quality. As the intestinal bacteria in the bioaerosols emitted from the WWTPs may pose a potential risk to onsite operators, aeration tanks in WWTPs should be paid more attention as a source of intestinal bacterial emissions.