This paper sampled the soils of Pinus sylvestris var. mongolica plantations in the Hulunbuir, the Horqin and the Mu Us Deserts. Combining field survey and molecular biology methods, this study analyzed the diversity of soil fungal communities by Illumina MiSeq high-throughput sequencing, and soil multifunctionality was calculated by the Z-score method as well as its influencing factors. The results indicated that 1) Soil organic carbon and hydrolyzable nitrogen of P. sylvestris plantations showed significant differences (Hulunbuir Desert> Horqin Desert> Mu Us Desert, P<0.05). Soil available cobalt in the Mu Us Desert was significantly higher than those in the Hulunbuir and the Horqin Deserts, while the soil available copper, available iron and available manganese were opposite (P<0.05). The soil multifunctionality of P. sylvestris plantations showed significant differences (Horqin Desert > Hulunbuir Desert > Mu Us Desert, P<0.05). 2) The species diversity of soil fungi in the Horqin Desert was the highest, Chao 1 and species richness index were significantly higher than those in the Hulunbuir and the Mu Us Deserts, and Shannon index was significantly higher than that in the Mu Us Desert (P<0.05). The phylogenetic diversity index of soil fungi in the Horqin Desert was the highest, which was significantly higher than that in the Hulunbuir and the Mu Us Deserts (P<0.05). Soil pH of P. sylvestris plantations showed significant differences (Mu Us Desert > Hulunbuir Desert> Horqin Desert, P<0.05); the soil electrical conductivity and soil moisture content in the Mu Us Desert were significantly higher than those in the other two deserts (P<0.05). The soil temperature in Hulunbuir Desert was significantly higher than those in the other two deserts (P<0.05). 3) The random forest model showed that altitude, longitude, latitude, pH, soil temperature, fungal Shannon index and species richness were important predictors for identifying soil multifunctionality, with an explanation of 83.68%. Geospatial factors had extremely significant positive effects on soil factors and soil multifunctionality (P<0.001), soil factors had significant negative effects on soil multifunctionality (P<0.05), and soil fungal diversity index had no significant effect on soil multifunctionality (P>0.05). The soil multifunctionality of P. sylvestris plantations in the Horqin Desert was the highest, and its soil ecosystem was more stable. Soil fungal diversity and abiotic factors drove soil multifunctionality of P. sylvestris plantations, but abiotic factors were more important than biotic factors. These results provide a better understanding of soil multifunctional characteristics of P. sylvestris plantations from the perspective of biotic and abiotic factors, as well as the rational utilization and scientific management of P. sylvestris plantations ecosystem.