Increasing studies indicated that multifunctionality, the ability of the ecosystem to provide multiple functions and services simultaneously, is driven by soil microbial communities. However, the role that the stability and network complexity of microbial communities play in maintaining ecosystem multifunctionality remains unclear, especially in the Arctic tundra, the ecosystem vulnerable and sensitive to climate change. Here, based on a survey comprising three sites in the sub-, low- and high Arctic, we estimated the relationships between multifunctionality and characteristics of soil fungal communities, including diversity, stability and network complexity. High-throughput sequencing with LSU and the NCBI database was used to identify the composition of fungal communities. Soil physical and chemical properties were determined, and plant composition and relative coverage were estimated. We also measured the soil respiration rate in situ to reflect the carbon flux. Multifunctionality was calculated based on 10 indicator variables of ecosystem functions, using average and multi-threshold methods. We hypothesized that a more stable and complex fungal community is positively associated with enhanced ecosystem multifunctionality, especially in the tundra with low coverage of vascular plants. Our findings will highlight the pivotal role of soil microbes in maintaining ecosystem functions and services, and provide novel insights into the resilience and adaptability of Arctic systems in the face of climate change.