In order to explore the abundance of soil ciliates in desert ecosystems, as well as the correlation between different soil aggregates, ciliate species/groups, and abundance, we collected soil samples from the central part of the Hexi Corridor, with sieving treatment. By analyzing and comparing the efficiency of the culture counting method and the Foissner counting method for quantifying protozoa, we also investigated the distribution and succession patterns of soil ciliates among different soil particle sizes. Results are as follows: ① The total abundance of ciliates obtained by the complete culture counting method was 16.5 times higher than that of the Foissner counting method, and the total number of ciliate taxa in the 10th day of culture was twice as high as that of the Foissner counting method; ② The total abundance of ciliates in soil aggregates of different grain sizes increased with the decrease of soil grain size. The abundance of ciliates in the 100-mesh soil sample was 3.4 times higher than that of the subsoil sample, while the abundance of ciliates in the in situ and 10-mesh soil samples increased with the decrease of soil grain size. The total number of ciliate species/taxa obtained from in situ and 10-mesh soil samples were higher than those from granular and 100-mesh soil samples; ③ The soil pH and moisture disturbance were the dominant factors in the change of ciliate abundance; ④ In the process of "non-submerged Petri dish method", the soil ciliate community showed a low-high-low pattern. As the most important structure of soil, soil aggregates play an important role in maintaining the structure of microbial community and enzyme activity in soil. It is suggested that when ciliate taxonomic research is carried out on soil in desert habitats in the future, the sieving of soil samples or the matching of re-examination dates should be tried for different taxa or target species. The complete culture counting method can not only record the number and abundance of various classes/taxa during the "non-submerged Petri dish" experiment, but also track the soil ciliate community succession, derive the "theoretical peak abundance" of species, and analyze the correlation between various taxa/groups and physico-chemical factors, as well as the relationship between ciliates and the physical and chemical factors. At the same time, we can analyze the correlation between various species/classes and physicochemical factors, which can provide a theoretical basis for the study of "Ciliatostasis", a ciliatostatic effect.