Gully erosion is one of the main causes of top soil loss, land deterioration and sources of sediment deposition in streams. Headcut often occurs in the gully erosion process when erodability of the soil layers varies, and the gully cuts through a hard layer at a point. A scouring hole appears downstream of the head cut which migrates upstream due to strong erosion in the scour hole. This paper presents numerical analyses of turbulent flow and sediment transport processes of a head-cut associated with a two-layer soil stratigraphic formation. The flow in the scour hole is three-dimensional induced by the water jet from the brink of the top layer; the sediment transport model considers sediment entrainment by the impinging jet, erosion underneath the hard layer and the retreat of the brink of the hard layer. The 3D flow simulation in the scour hole and the scouring process was verified with physical model data. The two-layer head cut migration is simulated with different flow and soil parameters, the trends of the simulated results reasonably revealed contributions of these parameters to the scouring and migration process.