Abstract: Deepwater riser/wellhead system is particularly vulnerable by external current to vortex-induced vibration (VIV). The bottom end of the subsea wellhead is usually simplified as a clamped constraint in the VIV analysis of deepwater riser/wellhead system. A three-dimensional VIV analysis model of the deepwater riser/wellhead coupling system is established in the in-line (IL) and cross-flow (CF) directions in this paper. The VIV analysis model takes the nonlinear pipe-soil coupling under wellhead into consideration. The time-varying nonlinear soil resistance generated by pipe-soil interaction is transformed into the time-varying equivalent stiffness of soil based on Hooke’s law. The soil equivalent stiffness is superimposed with the structural stiffness of the riser/wellhead system. The VIV analysis model is discretized by finite element method, and VIV numerical solution is performed with Newmark-β method and fourth order Runge-Kutta method. The effects of pipe-soil coupling and environmental factors such as current velocity and soil hardness on VIV characteristics of the deepwater riser/wellhead system are subsequently studied. The results show that the constraint of the deepwater riser/wellhead system under the pipe-soil coupling is weakened, and the overall stiffness and natural frequency of the system are reduced. The root-mean-square (RMS) displacement and vibration amplitude of the deepwater riser/wellhead system in the CF and IL directions have an increase, while the vibration frequency decreases. The VIV of the deepwater riser/wellhead system has a low sensitivity to soil hardness, because the system structural stiffness and the initial additional equivalent stiffness of the soil are large, while the second additional equivalent stiffness due to the soil hardness changes accounts for a relatively low proportion of the total system stiffness.