<p>The occurrence of apple replant disease (ARD) is closely related to the increase of soil pathogenic fungi abundance. However, the relationship between ARD and fungal community structure remains poorly understood. In this study, Illumina high-throughput sequencing was used to investigate the composition, diversity, and function of rhizosphere fungal communities associated with healthy (HRS) and diseased apple trees (DRS). Microbial taxa related to ARD were also identified. The severity of ARD varied among the sampled orchards. We found that Ascomycota was the dominant phylum in the DRS fungal taxa, and the fungal community abundance and Simpson index of DRS were significantly higher than those of HRS. Cluster and FUNGuild database analyses revealed significant differences in the relative abundance and function of fungal taxa between DRS and HRS. Most fungi isolated from DRS were plant pathogens, predominantly from the genus <i>Fusarium</i> (Ascomycota, Nectriaceae), which was also the predominant fungal genus detected in DRS. In contrast, <i>Mortierella</i> was more abundant in HRS. To validate the sequencing results, <i>Fusarium</i> isolates, including <i>F. proliferatum</i>, <i>F. oxysporum</i>, and <i>F. solani</i>, were verified as pathogens and showed high virulence. Structural equation modeling indicated that the occurrence of ARD was directly or indirectly influenced by <i>Fusarium</i>, <i>Mortierella</i>, phloridin, available phosphorus, and soil organic matter. Further research is needed to elucidate how soil parameters affect ARD. Laboratory tests demonstrated that <i>F. proliferatum</i> MR5 can produce pectinase and cellulase and is sensitive to two fungicides: flusilazole and bromothalonil. In conclusion, the deterioration of rhizosphere fungal community structure may be a key biological factor driving ARD, with <i>Fusarium</i> in DRS identified as a major causative agent of ARD in China. The findings of this study provide valuable insights for developing preventive strategies against ARD.</p>