Biological crust is a kind of ground cover which distributes widely. Due to their special physiological mechanisms, algae and moss can thrive and grow under the extreme cold and low light conditions so as form crusts. Biological crust (BSC) exists in various types of climatic region, soil and vegetation, the type of crust reflects the local water conditions and soil nutrient status, meanwhile, the formation of biological crust has an important influence on the occurrence and development of soil, hydrology and erosion processes, affects the physical and chemical properties of the soil, which manifests as the degree of influence of different types of crusts. However, the effect of biological crusts on soil infiltration is still controversial, on the one hand, biological crusts increase the roughness of the soil surface and correspondingly extend the retention time of water on the soil surface, which is not conducive to water infiltration, on the other hand, biological crusts improve soil structure and create water flow channels that are conducive to water infiltration. In this study, we used indoor simulation experiments, took the cyanobacteria crust-covered soil as research object to study the response characteristics of three relatives of soil under different freeze-thaw cycles and initial water contents, then quantitatively analyzed the trend and change point of the saturated hydraulic conductivity of crust-covered soil (Ks). The results show that the initial water content has no significant effect on Ks (P>0.05), and the number of freeze-thaw alternation has a very significant effect on Ks (P<0.01). The average Ks of bare soil under freeze-thaw conditions is 1.941 mm/min, the average Ks of crust-covered soil is 0.325 mm/min, and there is a very significant difference between them (P<0.01). With the increase of the number of alternation, the difference of Ks gradually increase, the Ks of bare soil reaches a maximum of 10.13 times of crust soil at 10 times. The Ks of crust soil under different initial water contents is approaching a similar level after 10-20 freeze-thaw alternations, with an average value of 0.219 mm/min. The effects of freezing and thawing significantly change the soil structure, especially after 7 times, and the soil particles lower than 0.1 mm, changing significantly. Under the experiment conditions, the degree of influence of Ks by the factors is as follows:number of freeze-thaw cycles > soil structure > crust thickness > crust bulk density > lower soil bulk density > initial freeze-thaw water content. The interactive effects of freeze-thaw cycles and crust thickness, crust bulk density, and the initial water content have the significant impact on Ks.