The flow pattern and its characteristics in the flood discharge stilling basin with step-down floors play dominant roles in effectively dissipating the discharged flooding water energy, guaranteeing the safety of the hydraulic structure and its downstream river bank stability as well as navigable flow conditions. A three-dimensional numerical model for water-air two-phase flows with strong nonlinearity, involving large free surface deformation and complicated solid-wall boundary conditions was established, and was applied to analyze flow characteristics in Xiangjiaba flood discharge stilling Basin with step-down floors. RANS(Reynolds-averaged Navier-Stokes) equations, Realizable k-ε turbulence model and VOF free surface tracking method were used in the developed numerical model. The model was firstly validated through comparisons of the simulated results and measured data for the flow patterns as well as the time-averaged pressure at the dam surface induced by the flood discharge jet. It is then applied to simulate the 3-D flow structure and fluctuation characteristics in the stilling basin with step-down floors induced by flood discharge from dam under the same discharge amount but different flood discharge scenarios. The results show that, for the flood discharge stilling basin with high and low step-down floors, under the same flood discharge condition, different scenarios of dam discharge gate open mode significantly affects the three-dimensional structure and characteristics of discharged flow in the dissipative pool induced by flood jets. The combined discharge from dam surface and middle holes results in the strong turbulent mixing of submerged multi-layer and multi-jet flows, effectively dissipating the energy of the discharged water and reducing the water surface fluctuations. The established numerical model can better reproduce the high-speed flooding jets and its turbulent motion in the dissipative pool associated with flood water discharge.