Soil microorganisms are crucial for the functional restoration of degraded ecosystems, largely depending on their interactions. Yet, the extent to which shifts in soil microbial co-occurrence patterns shape ecosystem functioning during the restoration of desertified ecosystems remains insufficiently elucidated. In this study, we systematically assessed temporal variations in soil microbial co-occurrence networks along a 53-year restoration chronosequence following the establishment of straw checkerboard barriers (SCBs) in the Tengger Desert of China. The results showed that the establishment of SCBs significantly reinforced microbial network complexity and stability, evidenced by increased number of nodes and edges, average degree, connectivity, clustering coefficient, and robustness, coupled with reduced average path length and vulnerability. The prevalence of positive links and cross-kingdom (bacteria-fungi) links also escalated with restoration duration. Soil microbial diversity showed significant correlations with network properties, indicating that enhanced diversity fosters more complex, cooperative, and structurally stable microbial networks. These microbial network properties were tightly coupled with ecosystem multifunctionality, wherein bacteria-fungi links and network stability emerging served as dominant direct drivers, while microbial diversity indirectly influenced multifunctionality via regulating microbial network structure. Collectively, our findings underscore that restoration efforts substantially advance ecosystem multifunctionality by reconfiguring microbial interaction networks, thereby illuminating microbe-driven mechanisms underpinning the ecological restoration of dryland ecosystems.