In order to analyze the influence of siltation height of check dam on overtopping Dam Breaking Flood, this work applies a hydrodynamic numerical model on a rectangular ideal channel and a realistic catchment to simulate the flow process of dam-break flood with different sediment thicknesses of check dam. The results showed that the flow of dam break decreases with the increase of siltation heights, and the relation between flood peak flow rate and silt thickness can be fitted by quadratic polynomial, with high fitting accuracy as correlation coefficient is around 0.99. When the sedimentation thickness reaches 20% or 40% of the dam height, the peak discharge reduction rate has reached 40.50% or 68.71%, respectively. Therefore, the reduction effect of siltation on peak flow is remarkable in the early and middle stages of siltation. Our results have guiding significance for the planning check dam system and the safety during flood season.