In order to study the root–soil composite system shear characteristics under the action of freeze–thaw cycles in the permafrost regions along the Qinghai–Tibet Highway (QTH) from the Beiluhe–Tuotuohe (B-T) section, the slopes in the permafrost regions along the QTH from the B-T section were selected as the object of the study. The direct shear test of root–soil composite systems under different amounts of freeze–thaw (F-T) cycles and gray correlations were used to analyze the correlation between the number of F-T cycles, water content, root content, and the soil shear strength index. The results show that the cohesion of the soil in the area after F-T cycles exhibits a significant stepwise decrease with an increase in F-T cycles, which can be divided into three stages: the instantaneous stage (a decrease of 46.73–56.42%), the gradual stage (a decrease of 14.80–25.55%), and the stabilization stage (a decrease of 0.61–2.99%). The internal friction angle did not exhibit a regular change. The root–soil composite system showed significant enhancement of soil cohesion compared with soil without roots, with a root content of 0.03 g/cm3 having the most significant effect on soil cohesion (increasing amplitude 65.20–16.82%). With an increase in the number of the F-T cycles, while the water content is greater than 15.0%, the greater the water content of the soil, the smaller its cohesion becomes. Through gray correlation analysis, it was found that the correlation between the number of F-T cycles, water content, root content, and soil cohesion after F-T cycles were 0.63, 0.72, and 0.66, respectively, indicating that water content had the most significant impact on soil cohesion after F-T cycles. The results of this study provide theoretical support for further understanding the variation law of the shear strength of root–soil composite systems in permafrost regions under F-T cycles and the influencing factors of plant roots to enhance soil shear strength under F-T cycles, as well as for the scientific and effective prevention and control of retrogressive thaw slump in the study area, the QTH stretches across the region.