As a frontier subject of nonlinear science, wave-current interaction has been studied by many scholars. This paper will explore the wave-current interaction under the serious sea conditions in the Northwest Pacific during the influenced by No.1 super Typhoon “Nepartak” in 2016. The results indicate that wave-current coupling model can effectively improve the simulation accuracy of significant wave height (SWH) under serious sea conditions. The influence of wave-current interaction on SWH is closely related to the angle between wave direction and sea surface current direction: when wave direction is close to current direction, wave-current interaction will decrease the SWH; in those areas where the wave and the current have the opposite direction, wave-current interaction will increase the SWH; the closer the angle between the wave and the current is to 90°, the less influence wave-current interaction has on the SWH. The maximum SWH difference whether including wave-current interaction or not is about 1.5 m.