Subduction of rough seafloor such as seamounts has an important influence on structure, geomorphology, stress, and seismic hazard of accretionary wedges. The Hikurangi subduction zone lies on the North Island of New Zealand, and the Hikurangi Plateau is subducting beneath the Australian Plate at a rate of 40–47 mm/a. Many seamounts of various shapes are distributed in the Hikurangi Plateau, whose subduction caused severe tectonic erosion along the northern Hikurangi Margin. In recent years, slow slip events (SSEs) have been well documented in seismology and geodesy at the Hikurangi northern margin. However, the evolution of tectonic erosion, structural stress regime, and their influences on seismicity remain unclear. By applying the discrete-element numerical simulation in combination with the interpretations of seismic reflection profile, the effects of seamount subduction on wedge geometry, fault structure, activity and strain distribution of the accretionary prism on the northern Hikurangi subduction margin were analyzed. The simulation result show that the subduction of a guyot seamount formed a mega-splay fault, which absorbed the substantial shortening and thrusts along the seafloor with low angle. With the subduction continued, a duplex shear zone was formed at the leading edge of the seamount, while the detachment moved down and extended forward to evolve into a frontal-thrust zone. Our simulations confirm that the seamount subduction enhanced the heterogeneity of the stress distribution within the forearc accretionary wedge, with significant accumulation of maximum shear stress at the leading edge of the seamount, while the rear edge of the seamount behaved as a stable stress shadow zone. The seamount subduction significantly increased the geometric roughness and material heterogeneity along the megathrust in the Hikurangi Margin, which has important implications for the generation of micro-earthquakes and slow slip events.