Purpose To curb and reverse the rapidly expanding desertification and enhance ecosystem functioning, various restoration strategies have been adopted in desertified regions of China. Optimizing those efforts requires an evaluation of their impacts on biodiversity and network complexity. However, the role of bipartite interaction between plants and rhizosphere microbes in driving the soil multifunctionality during restoration is poorly understood. Methods We examined the rhizosphere bacterial and fungal diversity associated with 14 plant species distributed along a 54-year chronosequence following the implementation of straw checkerboard barriers in the Tengger Desert, China. We also analyzed the architecture of bipartite interaction networks and relationship with soil multifunctionality. We used 12 soil functions relating to the C, N and P cycling to assess soil multifunctionality. Results Our findings revealed a significant increase in soil multifunctionality (p < 0.001) and fungal diversity (p < 0.01) during restoration. In contrast, bacterial diversity did not follow this pattern; instead, declined sharply during late restoration stage. The plant-fungi bipartite network properties exhibited a significant increase, followed by enhancing the soil multifunctionality (p < 0.05). In addition, at functional diversity level, the OTU richness of fungal saprotrophs associated positively with soil multifunctionality (p < 0.001). Consistent with diversity, the architecture of plant-bacteria bipartite network exhibited no significant directional shifts during restoration and showed minimal functional coupling to soil multifunctionality. The structural random forest modelling approach further confirmed these results, accounting for 70.01% variation and identifying fungi as key driver of soil multifunctionality. Conclusion Our research underscores the effectiveness of artificial straw checkerboard barriers in enhancing the fungal diversity-soil multifunctionality relationship mediated by plant-fungi association during restoration.