Aimed at the specialties of infiltration head higher and varying under the condition of water storage pits irrigation, numerical model of 3-D infiltration and the soil moisture movement of complicated boundary conditions in water storage pits was established. ADI method and Gauess-Seidel iterative method were used in numerical simulation followed by verification tests. The results showed that the calculated values were in accordance with the experimental results. This indicated the numerical model was correct and the method of solution was feasible.