Based on the coupling solution framework of three-dimensional incompressible Navier-Stokes equation and sediment transport model, this study uses SST k-ω turbulence model to close the flow equation, and combines the bed load and suspended sediment motion model to study the local scour evolution law of gooseneck structure of submarine pipeline under the action of water flow. By analyzing the time evolution characteristics of bed shear stress distribution, scour process and scour depth, the influence mechanism of gooseneck geometric characteristics on local scour is revealed. The results show that the flow field disturbance caused by the gooseneck structure significantly changes the spatial distribution of scour, and the scour characteristics of the contact area of the pipeline bed and the area below the gooseneck transition section are significantly different. The initial scour rate in the contact area of the bottom bed of the pipe is faster, but with the adjustment of the flow field structure, the scour rate gradually decreases, while the deeper and wider scour pits are formed in the area below the gooseneck due to the diversion effect.