Fungi community structure in paddy soils in south Jiangsu under different gradients of heavy metal pollution was analyzed in order to study the impact of heavy metal pollution on the microbial variability. The results showed that heavy metal pollution has significant impact on fungi number and community structure in paddy soil. Principal coordinate analysis (PCoA) revealed that the first and second components accounted for 35.96% and 21.48% of contribution rates, respectively. The results of redundancy analysis (RDA) showed that Pb and Cu greatly influenced fungi community structure. Relative abundance analysis of fungi at genus taxonomic level showed that heavy metal pollution significantly reduced the population of sensitive fungi but increased the population of patience fungi. Sensitive fungi genus included Mortierella, Trichoderma, Apodus and Hypholoma, wheras patience fungi genus included Paraglomus, Tetracladium and Rhizophydium. In conclusion, heavy metal-contamination can significantly influences soil fungi community structure in paddy soils, increasing heavy metal concentration can increase the population and diversity of heavy metal tolerant fungi and decrease sensitive fungi, which furtherly increases the differentiation of the structure of fungi community.