A novel three-stage integrated biofilter (TSIBF) composed of acidophilic bacteria reaction segment (ABRS), fungal reaction segment (FRS) and heterotrophic bacteria reaction segment (HBRS) was constructed for the treatment of odors and volatile organic compounds (VOCs)from municipal solid waste (MSW) comprehensive treatment plants. The performance, counts of predominant microorganisms, and bioaerosol emissions of a full-scale TSIBF system were studied. High and stable removal efficiencies of hydrogen sulfide, ammonia and VOCs could be achieved with the TSIBF system, and the emissions of culturable heterotrophic bacteria, fungi and acidophilic sulfur bacteria were relatively low. The removal efficiencies of different odors and VOCs, emissions of culturable microorganisms, and types of predominant microorganisms were different in the ABRS, FRS and HBRS due to the differences in reaction conditions and mass transfer in each segment. The emissions of bioaerosols from the TSIBF depended on the capture of microorganisms and their volatilization from the packing. The rational segmentation, filling of high-density packings and the accumulation of the predominant functional microorganisms in each segment enhanced the capture effect of the bioaerosols, thus reducing the emissions of microorganisms from the bioreactor.