Linkages between microbial communities and multiple ecosystem functions are context-dependent. However, the impacts of different restoration measures on microbial communities and ecosystem functioning remain unclear. Here, a 14-year long-term experiment was conducted using three restoration modes: planting mixed grasses (MG), planting shrub with Salix cupularis alone (SA), and planting shrub with Salix cupularis plus planting mixed grasses (SG), with an extremely degraded grassland serving as the control (CK). Our objective was to investigate how ecosystem multifunctionality and microbial communities (diversity, composition, and co-occurrence networks) respond to different restoration modes. Our results indicated that most of individual functions (i.e., soil nutrient contents, enzyme activities, and microbial biomass) in the SG treatment were significantly higher than in the CK treatment, and even higher than MG and SA treatments. Compared with the CK treatment, treatments MG, SA, and SG significantly increased the multifunctionality index on average by 0.57, 0.23 and 0.76, respectively. Random forest modeling showed that the alpha-diversity and composition of bacterial communities, rather than fungal communities, drove the ecosystem multifunctionality. Moreover, we found that both the MG and SG treatments significantly improved bacterial network stability, which exhabited stronger correlations with ecosystem multifunctionality compared to fungal network stability. In summary, this study demonstrates that planting shrub and grasses altogether is a promising restoration mode that can enhance ecosystem multifunctionality and improve microbial diversity and stability in the alpine degraded grassland.