Abstract:[Background] Organic pollution has a great impact on the microbial diversity of sediment. At present, there are few studies on the fungal community of sediment in polluted water. [Objective] To study the diversity characteristics of fungal community in the sediment of different degrees of organic pollution, and explore the influence of industrial organic pollution on the community structure of fungi. [Methods] Chemical analysis and high-throughput sequencing was adopted to study, and the relationship between environmental factors such as water quality, components of sediment and fungal diversity was analyzed. [Results] With the decrease of pollution degree, the number of fungal sequences, OTU and Shannon index in sediment were all increased. Unclassified Fungi, Ascomycota and Basidiomycota were the dominant species of the fungal community in the sediment. Zopfiella, Westerdykella, Clypeosphaeria, Ilyonectoria, Paracremonium and Aspergillus were the main dominant genera in sediment. Shannon index was significantly correlated with DO of water body, negatively correlated with organic matter and total phosphorus content of sediment. Simpson index was significantly correlated with TN, NH3-N and TP of water body. [Conclusion] Organic pollution leads to the decrease of dissolved oxygen in water and the increase of organic matter in sediment, which finally leads to the significant decrease of fungal diversity in the polluted area. Zopfiella, Penicillium, Emericellopsis, Westerdykella, Jugulospora and Chromelosporium may be mainly involved in the removal of pollutants in the aeration treatment area under facultative condition. Ilyonectria, Mortierella and Epicoccum maybe mainly involved in the decomposition of aquatic organism residues and the adsorption and settlement of pollutants.