In order to simulate the flood wave propagation through the breaches，a two-dimensional hydrodynamic model was developed. Roe method of unstructured mesh was used to solve the 2D model. Based on the actual characteristics such as linear features in the flood protected zone，ways and irrigation ditches were generalized to broad crested weir for calculation and endowed real height，considering it as special border and coupled unstructured mesh. Using the Natural Neighbor Interpolation， separated interpolation was conducted between protected zone and aqueduct，and terrain of aqueduct in the area was recovered，and model with real terrain was obtained through the above methods. The model was applied to the case of Qingtongxia West Irrigation of Yellow River on Sipaikou，effectively simulated water blocking of special border such as ways and irrigation ditches and water flow of bridge culverts，and the effect of drain in the aqueduct and intrusion in the estuary，and truly simulated the flood wave propagation and inundation area of flood in calculation area，thus the paper has bright application value.