Exploring the characteristics of soil properties, fungal communities, and their driving factors in different microgeomorphic units in arid gravel desert areas is important for the study of fungal community construction mechanisms and practical guidance for targeted ecological damage restoration strategies. In this paper, the changes in soil physicochemical properties, fungal α diversity, and community composition of four microgeomorphic units (wind erosion residual hills, gravel desert Gobi, river valley, and wind sand land) in an arid gravel desert area were compared. The main factors affecting soil fungal communities in different microgeomorphological units in gravel desert areas were explored by combining plant characteristics and micrometeorological factors. Results showed that the soil in the arid gravel desert area was dominated by sandy soil, and wind sand land had the largest sandy content and the smallest clay content, which was contrary to the soil mechanical composition of the river valley. No significant difference in soil bulk density and organic matter content was found between the river valley and the gravel desert Gobi, but their soil bulk density and organic matter content were significantly higher than those of the other two microgeomorphic units. However, the soluble salt content of the river valley was 21.4%, which was significantly lower than that in other microgeomorphic units, but the soil water content was significantly higher by 39.3%. Except for the contents of available N, available K and available P in the gravel desert Gobi and wind erosion residual hills, no significant difference in the available nutrients was found in other microgeomorphological units. In addition, the α diversity of soil fungi, Shannon-Wiener index, Pieloue index, and Simpson index all showed a significant decrease in wind sand land, whereas no significant difference in other microgeomorphological units was found. However, the Chao1 index has no significant difference. At the phylum level, the dominant fungi phyla were Ascomycota and Basidiomycota in different microgeomorphic units. Ascomycota has the largest dominance in the gravel desert Gobi and wind erosion residual hills, and Basidiomycota has the largest proportion in the river valley. At the genera level, Neocamarosporium and Subramaniu in the Wind erosion residual hill, Preussia and Neocamarosporium in the gravel desert Gobi, Aspergillus and Alternaria in the river valley, and Trichophaeopsis and Neocamarosporium in the wind sand land were the dominant genera of soil fungal communities in each geomorphic unit. Soil water content, organic matter, available N, and soluble salts were the common key factors affecting the changes in soil fungal community structure in different microgeomorphic units in an arid gravel desert area. Furthermore, the soil mechanical composition in wind sand land, surface temperature and light radiation intensity of wind erosion residual hills, surface wind speed of gravel desert Gobi, and surface vegetation biomass of river valley were the differentiated ecological factors affecting soil fungal community in each geomorphic unit.
