Abstract: In order to optimize the program of mulched drip-irrigation with brackish water for cotton, a soil water and salt numerical model with the root water uptake item was built by using HYDRUS. The parameters were identified and model was verified using the data of field experiments. The verified model was used to set up proper irrigation program of mulched drip-irrigation at cotton growth season and the flood irrigation at non-growth season for leaching soil salt, and to predict soil water and salt migration characteristics and its long-term effect. The results showed that the simulation matched observation well and the calculation rate was fast. The simulated and observed soil water and salt had no significant difference by T test. The parameters α and n had more notable influences on soil water than other parameters, while the longitudinal dispersivity DL had notable influence on soil salt. The proper program of mulched drip-irrigation in the study area is that two pipes are set up for one tarp with low irrigation water quantity and high irrigation interval combined with once flood irrigation during non-growth season for one or two years. Twenty-year simulation showed that the irrigation program would not result in soil secondary salinization.