To test the variation and transport of soil salinity in saline-alkali land under water storage and drainage treatments, an experimental model was established in Fuping, Shaanxi Province, 2009. The variation of soil salinity during 0—160 cm soil depth under the two treatments was determined and analyzed. Results showed that the average soil water content under water storage treatment was 4.47% higher than that under drainage treatment, which means that the water storage treatment could help to improve soil moisture to satisfy the crop’s growth needs. The profile distribution of soil soluble solids (TDS), anion (Cl-, HCO3-, SO42-) and cation (Ca2+, Na+, K+) content and the variation of soil pH were also measured and analyzed. PCA (Principal Component Analysis) was used to explore the relationship between the soil salinity and its ions, which showed that the water storage treatment could significantly decrease the surface salinity of soil and accelerate the desalination of topsoils, and finally, the soil quality was improved significantly, demonstrating that the water storage treatment has a remarkable effect on soil salinity management.