[Objective] The structure and diversity of soil microbial community and their changes reflect the quality of soil. To study the effects of a fertilizer synergist, we analyzed fungal communities from potato rhizosphere soil. [Methods] We used high throughput sequencing technology to sequence the fungi metagenomic DNA of the fungal internal transcribed spacer 1 (ITS 1) in the roots of potatoes. With the aid of RDP classifier, all rhizosphere soil fungi were identified from the reads of OTUs. [Results] Sequencing data suggested that after the quality control, 437 375 reads were remained. Cluster similarity analysis was performed with threshold of 97% sequence similarity, yielding 633 OTUs from the 12 samples. Phylogenetic analysis showed that Ascomycota were predominant in all samples (relative abundance from 56.95% to 97.23%). Ascomycota in all samples but Haiyuan with Novel Fertilizer Synergist increased. However, Basidiomycota decreased. Alpha diversity analysis showed that the fungal community diversity of the rhizosphere soil in the same site was different after fertilizer synergist application. however, in beta diversity analysis, no significant differences were observed with respect to fungal community composition, which could be attributed to the discrepancy in soil properties from different sampling sites. [Conclusion] Soil characteristics are one of the important factors in explaining the variation of microbial diversity. Fungal communities could be greatly changed by using Novel Fertilizer Synergist.