Heavy metal contamination is one of the most concerned global environmental problems and the soil heavy metal contamination is especially severe in lead-zinc mining areas in China. In order to study the soil fungal community composition changes responding to different degree of heavy metal pollution, soil samples from the lead-zinc mine field of Yunnan Mengnuo were studied. 5 samples from the heavy metal pollution soil (HP) and other 4 from the low pollution (LP), based on the cluster analysis of heavy metal contents and the physical and chemical properties of the sample were analyzed. Genomic DNA of the soil samples were extracted and the Internal Transcribed Spacer (ITS) genes were sequenced by the high-through sequencing Illumina MiSeq. The fungal communities at different taxonomic levels (Phylum, Class, Order, Family, Genus and Species) were compared. In HP samples, the abundance of unclassified fungi were the highest, then followed by Aspergillus, Un--s-Clavulinaceae sp. and Un--s-fungal sp. ARIZ L453 respectively. In LP samples, the unclassify fungi were also high, but less than HP. The relative abundance of fungi from high to low was Geastrum, Aspergillus and Mortierella. The Representational Difference Analysis (RDA) showed that different heavy metals influence fungal community diversity and the concentrations of Pb was significantly correlated with fungal community.