Abstract: Abstract: The Shiyang River Basin is an interior river basin that faces excessive water explore and utilization, outstanding contradiction between water demand and water resources and environmental deterioration in arid Northwest China. The groundwater is an important resource for social and economic development, maintaining the ecological environment and agricultural irrigation. Due to excessive exploration, the groundwater salinity increases year by year. In order to make up the shortage of fresh water resources and ensure the steady development of agriculture in arid district, saline water and deficit irrigation has been widely used in agricultural production. In order to understand the soil water and salt transport under the condition of deficit irrigation with saline water, the agro-hydrological Soil-Water-Atmosphere-Plant (SWAP) model was calibrated and validated to simulate water-salt transport and grain yield of maize based on the field experiments and observed data in in 2013. At the same time, the soil water flux and salt flux were simulated by SWAP model under the condition of deficit irrigation with saline water. The results showed that SWAP model better reflected the change tendency of the measured values at the process of soil water calibration and validation. The RMSE values of every soil profile were less than 0.04 cm3/cm3 and the MRE values were less than 10%. Therefore, the calibrated and validated SWAP model described water transport effectively. At the process of soil salt calibration and validation, the simulation values reflected the change tendency of the measured values perfectly. The RMSE values at variable dates were less than 2.0 mg/cm2 and the MRE values were less than 23%. Therefore, the calibrated and validated SWAP model reflected the effect on soil salt distribution by different irrigation conditions under the deficit irrigation with saline water effectively. At the process of grain maize yield calibration and validation, the simulation yield reflected the change tendency of the measured yield. Therefore, the calibrated and validated SWAP model reflected grain yield of maize under the deficit irrigation with saline water effectively. The simulation result of soil water flux showed that at the seedling stage of maize, the soil water flux above 40 cm was mainly upward and the flux mainly downward at the irrigation and rainfall stage. As the result of soil water flux of 60 cm under the deficit irrigation, it produced the deep leakage under the experimental conditions. The simulation result of soil salinity flux showed that it was similar between the soil water and soil salt transport. In seedling stage of maize, the soil salinity flux above 40 cm soil layer was given priority to upward because of the soil evaporation. In the stage of rainfall and irrigation, the soil salinity flux in all soil profile was mainly downward. The result of soil salinity flux at 60 cm showed that the salt brought by saline water irrigation could migrate to deep soil with the rain and leaching and it did not produce salt accumulation at the surface soil. The research results of this paper can provide valuable information for formulating deficit irrigation schedule with saline water.