【Objective】Grazing is one of the most important, simplest, and most economical ways of grassland utilization in the Inner Mongolia desert steppe. It is an important factor affecting plant, biological, and soil environmental changes. Soil protists play an important role in the material cycle and energy flow of desert steppe ecosystems, but little is known about how the protists respond to changes in grazing intensity. 【Method】A randomized block experiment was conducted in a Stipa breviflora desert steppe to analyze the diversity and composition of soil protist communities. Four treatments were set up: CK (Control), LG (Light grazing), MG (Moderate grazing), and HG (Heavy grazing). High-throughput sequencing technology was used to analyze the diversity and composition of soil protist communities. Combined with the analysis of vegetation characteristics and soil physical and chemical properties, the key environmental factors driving the change of soil’s protist biological community were explored. 【Results】The results showed that the soil protist communities in the Stipa breviflora desert steppe were mainly composed of Unclassified-Eukaryotes, Cryptophyta, Chlorophyta, Arthropoda, Streptophyta and Mucoromycota. The dominant groups (relative abundance accounted for 20% or more of the total abundance) were Unclassified-Eukaryotes and Cryptophyta. The common groups (relative abundance accounted for 2%-20% of the total abundance) were Chlorophyta, Arthropoda, Streptophyta, and Mucoromycota. The rare groups (relative abundance accounted for 2% or less of the total abundance) were Chytridiomycota, Apicomplexa, Chordata, and Basidiomycetes. Among these, the dominant groups and common groups were more sensitive to the change in grazing intensity. Grazing intensity changed the vegetation characteristics, soil physical and chemical properties, and soil protist community diversity of desert steppe. The Margalef richness index, Shannon-Wiener diversity index, Pielou evenness index, and biomass of vegetation were sensitive to the changes in protist communities. The total porosity, bulk density, organic matter, total nitrogen, total phosphorus, available phosphorus, available potassium, and pH were the key soil factors affecting the protist community. 【Conclusion】In conclusion, grazing affects soil protist communities by changing vegetation characteristics and soil environmental factors. Our results prove that there is a strong connectivity between protist and environmental factors in ecosystems with relatively scarce nutrient resources and clarify the protist groups that are sensitive to changes in grazing management measures in desert steppe.