A three-dimensional numerical simulation was carried out on the complex flow field in a stilling basin of multi-horizontal submerged jets (MHSJs) using the mixture renormalisation group κ–ε turbulence model. Emphasis was placed on the characteristics of the vortex structure in a stilling basin of MHSJs. The results show that vortices with horizontal axes under the main jets are more stable in a flood discharging through crests overflowing orifices and mid-discharge orifices than in a joint flood discharging through crest overflowing orifices and mid-discharge orifices, but the eddy with horizontal axis does not penetrate entirely through the water body along the spanwise direction in the stilling basin. For three typical operating conditions examined, vertical vortices between the main jets do not reach the slab of the stilling basin, but, instead, disappear into the water body; a vertical vortex formed under the main jets does, however, reach the slab of the stilling basin. The range and intensity of the vortices near the drop, side wall and slab of the stilling basin are small and weak, and the intensity of the vortex structure has little effect on the stability of the drop, side wall or slab of the stilling basin.