In ocean engineering, interactions between ocean currents and risers lead to regular vortex shedding on both sides of the riser, causing structural deformation. When the frequency of vortex shedding approaches the natural frequency of the structure, resonance occurs, significantly increasing deformation. This phenomenon is a critical cause of riser failure. Therefore, the dynamic response of flexible risers to vortex-induced vibrations (VIV) is crucial for their structural safety. This paper employs the finite-volume method to integrate over control volumes to solve for forces, such as pressure and shear stress, on the surface of the riser, while the finite-element method discretizes the continuous structural body into elements and nodes to solve for structural displacements and stresses. A strongly coupled method is utilized at each timestep to iteratively transfer load-displacement data between the fluid and structural fields, updating the boundary conditions of the fluid domain to achieve a bidirectional fluid–structure interaction simulation of vortex-induced vibrations in a seawater environment for flexible risers. The study finds that the three-dimensional flexible riser exhibits multi-frequency vibration phenomena and broadband vibration response characteristics under high flow velocity conditions. As the flow velocity increases, the vortex-shedding mode is observed to transition from the simple two single (2S) mode to the more complex pair + single (P + S) and two pair (2P) modes. In addition, the stiffness at the ends is enhanced by the fixed boundary conditions, and the coupling between the natural frequency of the ends and the vortex-shedding frequency triggers complex vortex-shedding phenomena in these regions. At higher flow velocities, these boundary effects result in more complex vortex-shedding modes and stronger vibration responses at both ends of the riser.