It is important to identify key microbial drivers of soil multifunctionality (SMF) under plant biomass incorporation in dryland agroecosystems. A two-year field experiment was conducted with three treatments, including plastic film mulching alone (PM), maize straw incorporated beneath plastic film (PMSM), and living white clover grown beneath plastic film (PMCM). Bulk soil and plastisphere samples were analyzed and SMF was quantified to assess the effects of bacterial and fungal diversity. Compared with PM, biomass incorporation with either maize straw or white clover significantly increased SMF, with PMSM showing the highest improvement (35.3%). Correlation analysis revealed that SMF was positively associated with bacterial diversity in bulk soil and plastisphere, as well as fungal diversity in the plastisphere, but negatively associated with fungal diversity in bulk soil. Relative weight analysis identified fungal diversity as the most influential biotic factor contributing to SMF. Random forest analysis further identified several low-abundance fungal taxa, such as Torula, Stachybotrys, and Trichoderma (Ascomycota), as well as Schizophyllum (Basidiomycota), as important positive predictors of SMF. Overall, this study highlights the pivotal role of fungal diversity, particularly low-abundance taxa, in enhancing soil multifunctionality in dryland agroecosystem, and provides scientific evidence for optimizing organic matter management in plastic mulched agriculture.