To study the effect of magnetic water irrigation on the improvement of different salinized soils and the growth of cotton in Xinjiang, field experiments were conducted in three salinity soils (slight, medium, and heavy salinity soils), with five intensities of magnetized irrigation water (0 GS (CK,G0), 1000 GS (G1), 3000 GS (G3), 4000 GS (G4), and 5000 GS (G5)). Magnetized irrigation water can change the distribution of water and salt in all salinized soils, increase the water holding capacity and salt leaching of soil, and reduce the soil salt contents in the soil profile. It is better for the improvement on slight saline soil was better than on medium and heavy saline soils; the G3 treatment had the strongest effect by increasing soil water content by 33.2%−56.2% and improving the desalination rate by 29.2%−50.4%, compared to the control. Magnetic water irrigation significantly increased cotton growth. A negative relationship was found between soil salt content and plant growth characteristics (plant height, stem diameter, leaf number, leaf area index, and chlorophyll SPAD). Under the different intensities of magnetic water treatment, cotton growth indexes showed the same trends: CK < G1 < G5 < G4 < G3 in all three salinized soils. (3) Compared with the control treatment, magnetic water treatment can increase cotton yield and water use efficiently. Maximum water use efficiency and yields were obtained when the magnetization was 3000GS, in which the water use efficiency was increased by 27.4–42.8%, and the yield was increased by 28.8–31.69% compared with control. In this region, irrigating with magnetized water with 3000GS could improve saline soil quality and cotton growth, especially in slight salinity soil.