Xinjiang is short on freshwater resources and rich in ones. The unregulated use of brackish water for agriculture leads to the aggravation of secondary salinization in soil; however, magnetization can improve the quality of brackish water. To evaluate the effects of magnetized brackish water drip irrigation on the water and salt transport characteristics of sandy soil in southern Xinjiang, China, a field plot experiment was carried out in which irrigation water was treated using one or two water magnetization events at different magnetization intensities. Water was treated at five magnetization intensities: 1000, 2000, 3000, 4000, or 5000 Gs, while unmagnetized water was used as the control. The results showed that the magnetization of brackish water used in drip irrigation decreased the water transport rate and increased the water holding capacity of the root layer soil. Magnetized irrigation water enhanced the leaching of soil salt and reduced the rate of salt accumulation. Compared with the control, the salt content of the magnetized water-irrigated soil decreased by 15.0%~33.7%, and the salt storage in the magnetized water-irrigated soil decreased by 44.99%~86.78%. The lowest rate of salt accumulation (4.96%) was observed at a magnetization intensity of 3000 Gs. Magnetized water irrigation changed the composition and proportions of soil ions, and Na+, Cl−, and SO42− leaching from the soil increased. The effect of magnetizing the irrigation water twice was greater than that of one magnetization event. Magnetizing the water twice at an intensity of 3000 Gs led to the largest decrease in the relative percentage contents of Na+ and Cl−, which were 80.90% and 82.36%, respectively. The magnetization intensity had a significant effect on the soil carbon and nitrogen contents, which showed a trend of first increasing and then decreasing as the magnetization intensity rose. The total carbon content after irrigation with magnetized water increased by 13.48%~63.35%, and the total nitrogen content increased by 11.73%~147.96%. The magnetization treatment of irrigation water can therefore reduce the risk of soil salinization and reduce salinity stress on crops in arid regions, providing a new method for alleviating the shortage of freshwater resources in Xinjiang and a means to use brackish water safely while improving salinized soil.