Understanding the assembly mechanism of fungal communities is of great importance for conserving and managing mycobiomes. However, the ecological processes underlying the decline in fungal community size remain poorly understood. Herein, we characterized soil fungal assembly processes at three community levels (stage-specific absent taxa, remaining taxa, and whole taxa) using ITS sequencing data. The bulk and rhizo-spheric soil samples were collected at five growth stages of soybeans, which grew in soil with 16-year fertil-ization. An alpha diversity analysis revealed that rhizospheric communities decreased fungal richness during the soybeans' developmental transitions. Some plant pathogens in the phylum Ascomycota showed stage-specific loss in the soybeans' rhizosphere. The neutral model explained 34-40 % of the demographic variations of the remaining subcommunities and the whole communities. Their assembly processes were primarily governed by dispersal limitation in both sampling compartments and secondarily governed by variable selection and drift in the bulk soil and rhizosphere, respectively. The temporally missing subcommunities were nonneutral and pri-marily dominated by drift. Moreover, both the highly connected network nodes and the temporally missing taxa promoted the attack robustness of fungal communities. Overall, these results advance our understanding of the assembly of different subsets of fungal communities and provide new insight into the maintenance mechanisms of metacommunity stability.