Elevated atmosphere CO2 (eCO2) levels lead to changes in the quantity and composition of rhizodeposition of soybeans. Previously, a majority of studies have focused on the bacterial community response to the eCO2 in the rhizosphere of soybean with little information regarding the quantitative and compositional changes in the fungal community available. To provide insight into the fungal community response, next generation sequencing of the internal transcribed spacer (ITS) region was conducted for in-depth analysis of changes in fungal abundance and diversity in response to eCO2. Four soybean cultivars (i.e. Xiaohuangjin, Suinong 8, Suinong 14 and Heinong 45) were grown for 65 days under ambient CO2 (aCO2) (390 ppm) and eCO2 (550 ppm) in Mollisol soils. Elevated CO2 significantly increased ITS copy numbers in the rhizosphere of the soybean cultivars except Xiaohuangjin and Suinong 14. Principal coordinate analysis (PCoA) revealed that eCO2, rather than soybean cultivars, altered the composition of soil fungal communities. Network analysis indicated that eCO2 simplified the network structure by changing topological roles of operational taxonomic units (OTUs) and key fungal members, which were likely regulated by concentrations of NH4+-N, NO3−-N and available K and microbial biomass C under eCO2.