The alpine grassland ecosystems of the core Sanjiangyuan region on the Qinghai-Tibet Plateau play a crucial role in addressing global climate change. In this area, both natural alpine grasslands and artificial grasslands have become the predominant land use types due to climate change and human activities. This study employed Illumina MiSeq sequencing to investigate the microbial communities in the surface soil across three grassland types: alpine grasslands (AG), alpine desertified grasslands (ADG), and alpine artificial grasslands (AFG). We aimed to explore the response patterns and intrinsic relationships among vegetation, soil, soil microbes, and ecosystem multifunctionality (EMF). Our findings revealed that alpine natural grasslands have higher vegetation diversity than AFG, which, despite having fewer species, possess significantly higher soil nutrient. These differences leads to distinct microbial community structures: ADG showed increase microbial variability, while AFG exhibits microbial homogenization. Prokaryotic communities are primarily influenced by deterministic processes, whereas fungal communities are mainly shaped by stochastic processes. Human disturbances can enhance EMF (AFG > AG > ADG) but may alter microorganisms' potential ecological connections and weaken fungal stability. In contrast, the resilience of natural grasslands and efficient aerobic processes in ADG support ecological recovery. In conclusion, although artificial grasslands can quickly improve certain functions, they cannot fully replicate the complex structure and benefits of native alpine grasslands. Thus, prioritizing native ecosystems protection and using artificial restoration as a supplementary strategy is recommended.