This study conducted numerical simulations of three-dimensional vortex-induced vibrations (VIV) on cylindrical bodies with various surface protrusion coverage rates, systematically investigating the impact of coverage and protrusion height on the vibrational response of flexible cylinders. The fluid forces on the surface of the riser were resolved using the finite volume method, while the structural forces were solved with the finite element method. A strongly coupled approach was employed for iterative updates between the flow field and structural field data, achieving a bidirectional flow–structure coupling simulation of VIV in a marine environment. The study further explored the performance of surface protrusions in suppressing VIV and considered protrusion heights of 0.1 times the cylinder diameter (0.1D) under coverage rates (CR) of 0%, 10%, 20%, 30%, and 40%, as well as seven different protrusion heights of 0.05D, 0.1D, and 0.15D at a 20% coverage rate. The mechanism of VIV suppression by surface protrusions was identified as altering the separation point of the shear layer and the frequency of vortex shedding through the vortices formed between the surface protrusions. It was found that a 20% coverage rate with a protrusion height of 0.01D (CR20) effectively suppressed the VIV of the cylinder, showing the best performance in VIV suppression, with an efficiency of 30.04%. These results provide a theoretical basis for designing more efficient VIV suppression devices and contribute to enhancing the resistance of marine structures against vortex-induced vibrations.