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Gravel mulching is a traditional method of water conservation in the semi-arid regions of China. In this study, we investigated the soil microbial community in a field in China’s Gaolan County which has been gravel mulching for over a period of 18 yr. Compared with the non-mulch control, total organic nitrogen (TON), microbial biomass carbon (MBC), and microbial biomass nitrogen (MBN) were all significantly increased in the field with gravel mulching for over 13 yr. Moreover, after 18 yr, the soil bulk density and sand content increased significantly, thus degrading the soil microenvironment. Gravel mulch significantly altered the bacterial community structure and composition, increased the abundance of Acidobacteria, Gemmatimonadetes, Bacteroidetes, and Firmicutes, and decreased the abundance of Actinobacteria compared with the control. Gravel mulch also significantly changed the fungal community structure and composition; the soils were found to have a greater abundance of Basidiomycota and Zygomycota and reduced abundance of Ascomycota and Glomeromycota compared with the control soils after long-term gravel mulching. Redundancy analysis (RDA) revealed that the bacterial genera after 18 yr of mulching were dominated by Incertae_Sedis, Blastocatella, Desulfovibrio, Bacteroides, Gemmatimonas, Parabacteroides and Alloprevotella, and that the composition of the bacterial community was related to soil pH, bulk density, MBC and MBN. However, significant decreases in the diversity indices of Chao1, abundancebased coverage estimator (Ace) and Shannon after 18 yr of mulching demonstrated negative effects on the complexity of the soil microbial community.