Abstract: Cotton is an important cash crop in Xinjiang, accounting for 90.2% of China's total production in 2022. However, natural factors such as drought, high soil salinity, and the constraints of perennial shallow tillage soil management practices limit the yield and efficiency of cotton production and sustainable agricultural development. Deep vertical rotary tillage facilitates the breaking up of soil solidification and promotes the salt leached by irrigation water. In order to investigate the improvement effect of deep vertical rotary tillage on heavily saline cotton fields in Southern Xinjiang of China, this study conducted a 2 a (2021-2022) field experiment with three deep vertical rotary tillage depths (DT20: deep vertical rotary tillage 20 cm, DT40: deep vertical rotary tillage 40 cm, DT60: deep vertical rotary tillage 60 cm), and alternate with conventional tillage (five-share plowing 20 cm CT20), and CT20 was set to be the two consecutive years of conventional tillage. Original soil samples from 0-60 cm were collected to determine the water-stable aggregates. Soil moisture, salinity, organic carbon, total nitrogen, total phosphorus and total potassium were defermined by samples under the drip irrigation tapes, wide rows and narrow rows of each treatment on the 3rd day after each irrigation. Cotton root samples were collected at 105 days after sowing in 2021 and at 103 days in 2022. The effects of different depths of deep vertical rotary tillage on soil physical properties, soil nutrient content, cotton root length density, boll weight, dry matter mass accumulation and seed cotton yield were investigated, and the effect of crop yield was quantified by structural equation modeling. The results showed that: 1) deep vertical rotary tillage was able to loosen the soil in the tillage layer to optimize the soil structure. DT60 treatment was able to significantly reduce the soil bulk density, the content of coarse aggregates (>2 mm), and silt and clay particle (<0.053 mm) in the tillage depth layer compared with DT20 and CT20 treatment, which led to a significant reduction in mean weight diameter and mean geometric diameter, and increased total soil porosity and the content of micro-aggregates (<0.25～0.053 mm), while DT60 treatment was unable to further improve the soil structure in the deep soil layer compared with DT40 treatment. 2) DT40 and DT60 treatments were able to significantly increase soil moisture from 0-40 cm soil layer and reduce soil salinity and pH value, whereas DT20 treatment was only able to reduce soil salinity from 0-20 cm soil layer, whereas DT60 treatment was able to significantly reduce soil salinity and pH value from 0-60 cm soil layer compared with DT40 treatment. The reduction of soil salinity promoted the accumulation of soil organic carbon in the 0-40 cm soil layer and soil total nitrogen in the 0-60 cm soil layer, but DT60 treatment was unable to significantly increase soil organic carbon and soil total nitrogen in the 0-20 cm soil layer compared with the DT40 treatment. 3) The analysis of the structural equation modeling showed that soil salinity was an indirect factor affecting the seed cotton yield, and the accumulation of cotton’s dry matter and the weight of cotton bolls were the direct factored. The reduction of soil salinity favors soil nutrient accumulation and cotton root growth, promoted nutrient transport and accumulation to the plant organ, and increased cotton dry matter accumulation and seed cotton yield. Therefore, DT60 treatment had the best effect of soil salinity reduction, and thus the effect of yield increase. Comprehensive analysis showed that the depth of 60 cm on deep vertical rotary tillage with conventional tillage alternating can realize the synergy of improving and increasing the yield and efficiency of the severe saline cotton fields in the Southern Xinjiang of China.