In order to understand the niche of dominant species of soil ciliates and its relationship with environmental factors at different altitudinal gradients on Kuizu Mountain, Bailang Village, Linzhou County in the Lhasa River Basin in autumn, a total of 11 sample sites were set on Kuizu Mountain in October 2015. Five-point pattern of plum blossom was adopted to collect soil samples with soil sampler, while the corresponding physical and chemical factors were recorded. Soil samples were brought to the laboratory for natural drying. Non-flooded petri dish method and in vivo observation were used for culture and morphological identification. A total of 132 species of soil ciliates were identified, belonging to 66 genera, 48 families, 14 orders, and 3 classes in the 11 sample points on Kuizu Mountain. There were 14 dominant species (Y＞0.02), among which the absolutely dominant species (Y＞0.1) were Glaucoma Scintillans and Litonotus carinatus. The largest niche width of the dominant soil ciliate species was Dileptus conspicuous. The smallest niche widths were Prorodon ovum and Colpoda simulans. The niche overlap of dominant species of soil ciliates ranged from 0.02 to 0.99. Colpoda simulans and Prorodon ovum had the lowest niche overlap, but Keronopsis monilata and Colpoda inflata had the highest niche overlap. The sum of the ecological response rates of the 14 dominant species was negative, indicating that the dominant species of soil ciliates were in a declining stage on Kuizu Mountain. The Canonical correspondence analysis(CCA) of dominant species and environmental factors of soil ciliates showed that, Axis 1 and 2 accounted for 37.8% of species variation, indicating that Axis 1 and Axis 2 could better reflect the relationship between dominant species and environmental factors, total nitrogen was a significant explanatory variable, the explanatory rate of dominant species variation was 17.6%. In conclusion, Dileptus conspicuus, Hemiophrys pectinata and Glaucoma frontata had strong adaptability to the soil environment and had a wide range of ecological adaptation. The niche overlap of dominant species of soil ciliates was low, the interspecific competition was weak. The relative dynamic balance between the dominant species of soil ciliates and the environment has not been reached, and the dominant species community was in a declining stage. Total nitrogen was the main environmental factor affecting the variation of soil ciliates dominant species community and the niche on Kuizu Mountain in the Lhasa River Basin.