Precipitation variability profoundly influences soil microbial diversity, community assembly processes, and co-occurrence networks. However, the responses of soil microbial structure to relative precipitation changes in alpine regions remain uncertain. To address this, we conducted a two-year field precipitation manipulation experiment in alpine steppe and alpine desert steppe ecosystems at the source of the Yarlung Zangbo River on the Tibetan Plateau. The experiment simulated 25%, 50%, and 75% increases and decreases in precipitation to examine how soil microbial communities respond to altered precipitation regimes. Our results reveal that microbial responses varied with precipitation magnitude, grassland type, and microbial kingdom. In the alpine steppe, bacterial alpha-diversity exhibited a negative asymmetric response to altered precipitation at both species and phylogenetic levels. Both bacterial and fungal species alpha-diversity tended to respond more strongly to changes in precipitation at high gradients in the alpine steppe than in the alpine desert steppe. Microbial co-occurrence networks in the alpine steppe were generally more responsive to altered precipitation than those in the alpine desert steppe. Furthermore, fungal alpha-diversity at both species and phylogenetic levels, as well as beta-diversity, responded more strongly to altered precipitation than bacterial communities. These findings suggest that precipitation-driven shifts in microbial community composition and network structure vary across alpine grassland ecosystems, with fungal communities exhibiting greater sensitivity than bacterial communities. As warming intensifies precipitation variability, these microbial shifts may have cascading effects on soil biogeochemical processes and ecosystem stability, underscoring the necessity for ecosystem-specific conservation frameworks and adaptive management strategies tailored to alpine grasslands.