Blockage through crossing structures is one of the dangerous problems that threaten its stability. There are few researches concerned with blockage shape in culverts and its effect on characteristics of scour downstream it. The study's purpose is to discuss the action of blockage through box culvert on both water surface and scour numerically. A sediment transport model has been investigated for this purpose using FLOW 3D v11.1.0. Different ratios of blockage through box culvert have been studied. The FLOW 3D model was calibrated with experimental data. The results present that the FLOW 3D program was capable to simulate accurately the scour downstream box culvert. The velocity distribution, maximum scour depth and water depths for blocked cases have been plotted and compared with the non-blocked case (base case). The results proved that the blockage ratio 70% of culvert height makes the water depth upstream increases by 2.3 times of culvert height and mean velocity increases by 3 times more than in the base case. An equation has been created to estimate the relative maximum scour depth as a function of blockage ratio