The distribution pattern and maintenance mechanism of biodiversity, namely community assembly are critical issues for the community ecology. A key issue in microbial ecology is quantifying the relative contributions of deterministic processes and stochastic processes to microbial community assembly. Although protists are an important part of the soil microbial communities and play a key role in the microbial loop, compared with bacteria and fungi, we know very little about the elevational distribution patterns and assembly mechanisms of soil protist community. In this paper, we used Illumina Miseq high-throughput sequencing technology to comprehensively analyze the community composition and diversity maintenance mechanism of soil protist community in the subalpine grassland ecosystem of Mount Wutai (altitude of 2000-3061 m above sea level). In total, 520673 valid sequences, which belong to 8 supergroups, 24 phyla, 65 classes, 125 orders, 222 families and 350 genera, were obtained from the soil of the four altitudinal gradients. Cercozoa, Ochrophyta, Ciliophora and Apicomplexa were the dominant soil protist phyla in the study area. LEfSe analysis showed that 17 biomarkers were very sensitive to elevation gradients, and different elevation gradients enriched different protist populations. The altitude had no significant effect on the α-diversity of soil protist community, but non-metric multidimensional scaling (NMDS) and similarity analysis (ANOSIM) indicated that the compositions and structures of protist communities were significantly different among the elevation gradients (P<0.05). Redundancy analysis (RDA) showed that elevation, soil water content, total nitrogen and plant richness were significantly correlated with protists community structure (P<0.05). Variance partitioning analysis (VPA) and partial Mantel analysis showed that both environmental factors and spatial variables had significant effects on the altitudinal gradient distribution pattern of protist communities, and the relative effect of environmental factors (7.9%) was significantly greater than that of spatial variables (1.8%).The Bray-Curtis distance between soil protist communities was significantly and positively correlated with the elevation distance (P<0.05), indicating that the selection process may be the main driving factor for the distribution pattern of soil protist communities in subalpine grassland. The Null-model analysis further confirmed that the relative role of deterministic processes in the assembly of soil protist communities was greater than that of stochastic processes. In conclusion, there were significant differences in the structure and composition of soil protist communities in Mount Wutai subalpine grassland along the elevation gradient, and the assembly mechanism was mainly determined by deterministic processes.