Abstract: Background The southern Xinjiang region experiences long and cold winters, with soil undergoing extended freezing periods. During this time, the interrelated dynamics of soil moisture, temperature, and salinity are complex. These processes not only influence soil structure but also significantly affect soil moisture conditions and the sowing environment after the spring thaw. Methods To investigate the effects of cotton stalk interlayer methods on soil moisture, temperature, and salinity dynamics under freeze-thaw conditions in southern Xinjiang, three treatments were established: surface coverage with cotton stalks, burial at 30 cm depth, and a control group with no addition. Two winter irrigation quotas (1800 m³/hm² and 2400 m³/hm²) were applied under experimental conditions to study the changes in soil moisture, temperature, salinity characteristics, and physical properties during the freeze-thaw period. Results Surface coverage with cotton stalks increased soil moisture content and temperature during the freeze-thaw process. The average moisture content in the 0–10 cm soil layer was 27.62% higher compared to the control group without cotton stalk addition, while the average surface temperature increased by 0.75°C. Higher winter irrigation quotas resulted in higher average soil temperatures during the freeze-thaw period. In the 0–5 cm soil layer, the salt content under surface coverage and 30 cm burial treatments was 42.38% and 75.69% of that in the control group, respectively. Winter irrigation quota had no significant effect on soil salinity (P > 0.05). In the 0–10 cm soil layer, soil bulk density under surface coverage and 30 cm burial increased by 3.37% and 0.69%, respectively, compared to the control. Porosity decreased by 2.14% and 0.56%, and saturated hydraulic conductivity decreased by 12.13% and 2.43%. Surface coverage with cotton stalks improved the ratio of solid, liquid, and gas phases in the soil. Soil under a winter irrigation quota of 2400 m³/hm² exhibited better development of preferential flow, while the cotton stalk interlayer suppressed the development of preferential flow. Conclusions The cotton stalk interlayer can mitigate soil salt accumulation and reduce the impact of freeze-thaw cycles on soil physical properties and structure, with surface coverage showing more pronounced effects. This study provides both theoretical support and practical applications for the utilization of cotton stalk resources and the promotion of efficient agricultural production in arid saline-alkali regions.