The characteristics of bacterial and fungal community changes in different treatment units of a pig farm was analyzed by Illumina high-throughput sequencing technologies. Their influence on those water quality parameters was inspected by means of redundancy analysis. The results show that the main bacterial groups in the activated sludge were Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria; After biological treatment, the content of Proteobacteria decreased by nearly 15%, while the one of Firmicutes dropped by nearly 6% from incoming water to out water, and in the meantime the content of Actinobacteria increased by almost 7%; the main fungi groups are Ascomycoka, Basidiomycota and a small amount of Chychomycetes. Its worth noting that after treatment, the effluent still contained abundant fungal pathogens such as Aspergillus, Trichosporon and Cladosporium, which can be potential threats to future environmental and public health. The variation of many bacterial and fungal community in swine wastewater treatment system is significantly affected by water quality parameters(mainly COD and nitrogen concentration).