Arbuscular mycorrhizal (AM) fungi can coexist with wetland plants and play an important role in the restoration and maintenance of wetland ecosystem. However, the distribution and influencing factors of soil AM fungal community under different environmental conditions in wetland ecosystem still need to be clarified. Therefore, this study used high-throughput sequencing technology to explore the effects of water level and vegetation type on the community structure and diversity of soil AM fungi in Poyang Lake wetland. Two typical plant communities (Triarrhena lutarioriparia and Persicaria hydropiper) under different water levels (high and low water level) were chosen to compare the difference of the community structure and diversity of AM fungi among different environmental conditions. The relationship between AM fungal community and soil physicochemical properties was analyzed. The results showed that the OTU number of AM fungi ranged from 21 to 38. Both water level and vegetation type affected the OTU number of AM fungi in Poyang Lake wetland. The OTU number of AM fungi was higher under high water level than that under low water level, and it was higher in P. hydropiper community than that in T. lutarioriparia community. The identified genera of AM fungi were Glomus, Claroidoglomus and Paraglomus. Among them, Glomus was the dominant genus, accounting for more than 85%. And the relative abundance of Glomus was significantly higher under high water level, compared with low water level, while it was significantly higher in T. lutarioriparia community, compared with P. hydropiper community (p<0.05). The AM fungal diversity indices (Simpson and Shannon index) were affected by water level, vegetation type and their interaction (p<0.01). Under low water level, there was no significant difference in AM fungal diversity indices between different communities, but under high water level, the AM fungal diversity indices in P. hydropiper community was significantly higher than that in T. lutarioriparia community (p<0.05). Water level had a higher effect on community structure of soil AM fungi than that of vegetation type, and vegetation type significantly affected AM fungal community structure only at low water level. Correlation analysis showed that there was no significant relationship between AM fungal diversity indices (Shannon and Simpson index) and soil factors. Dominant genera Glomus and OTU number were significantly and negatively correlated with soil water content at low water level (p<0.05), while Glomus was significantly and positively correlated with soil pH at high water level (p<0.05). Hence, there was a threshold effect of soil water content on Glomus in wetland ecosystem. The results of the present study could provide scientific guidance for the restoration of degraded wetland ecosystem.