Fungi are widely distributed in all terrestrial ecosystems, and they are essential to the recycling of nutrients in all terrestrial habitats on earth. We wanted to determine the relationship between soil fungal communities and geochemical factors (geographical location and soil physicochemical properties) in three widely separated geographical regions (the Antarctic, Arctic, and Tibet Plateau). Using high-throughput Illumina amplicon sequencing, we characterized the fungal communities in 53 soil samples collected from the three regions. The fungal richness and diversity indices were not significantly different among the three regions. However, fungal community composition and many fungal taxa (Thelebolales, Verrucariales, Sordariales, Chaetothyriales, Hypocreales, Pleosporales, Capnodiales, and Dothideales) significantly differed among three regions. Furthermore, geographical location (latitude and altitude) and six soil physicochemical properties (SiO₄²⁻-Si, pH, NO₃⁻-N, organic nitrogen, NO₂⁻-N, and organic carbon) were significant geochemical factors those were correlated with the soil fungal community composition. These results suggest that many geochemical factors influence the distribution of the fungal species within the Antarctic, Arctic, and Tibet Plateau.