Traditional surface irrigation simulation models are based solely on the one-dimensional long wave equations, irrespective of the hydraulic performance under the varied-discharge irrigation system. The movement process of surface water flow in varied-discharge border irrigation system was analyzed, which was divided into five stages according to different boundary conditions: constant inflow stage, variable inflow stage, border head recession stage, field surface recession stage 1, and field surface recession stage 2. A numerical simulation model for varied-discharge border irrigation was developed by simulating the border irrigation system of rapidly varied discharge based on the continuity equation and the momentum equation of rapidly varied flow. The proposed model was validated by field experiments with two sets of constant-discharge border irrigation and four sets of varied-discharge border irrigation, as well as two of sets border irrigation experimental data in the literature. It was observed that in all border irrigation experiments, the proposed model reasonably agreed with field measurements. The coefficients of determination values were all greater than 0.96 for the simulated advance times, and greater than 0.90 for the simulated recession times. Compared with the commonly used WinSRFR model, the proposed model had similar accuracy in simulating constant-discharge border irrigation and higher accuracy in simulating varied-discharge border irrigation. The proposed model accurately simulated the inflow movement of varied-discharge border irrigation, thus providing a guarantee for optimizing the design of varied-discharge border irrigation system.