The oscillation of steel catenary riser (SCR) would develop a trench in a few months, while the trench could affect the structural behavior of the riser in turn. However, the influence of the trenches on the fatigue damage of SCR is still controversial. In this study, the SCR model is established using the vector form intrinsic finite element (VFIFE) method, integrated with the nonlinear seabed model to develop the trenches. Different static platform offset distributions, low frequency (LF) surge motions, and the soil parameter and heave motion amplitude combinations are selected to investigate the influences on the trench formation. Dynamic analyses are performed to determine the effects of the trenches on the mechanical behavior of SCR based on the VFIFE model, with the predefined trenches inputted previously through the switching method and the inserting method. Simulation results prove that the trenches developed only by heave motion or including the LF surge motion have a positive effect in reducing the fatigue damage, while the trenches considering static platform offset have little influence. Furthermore, the effects of shear strength distribution of trench surface, trench depth, and trench position on the dynamic performance of SCR are discussed.