In this study, we present a three-dimensional numerical model for the interaction of flow with submerged flexible vegetation, based on a large-eddy simulation and the immersed boundary method. The model innovatively realises the interaction between the flow and highly flexible vegetation with clustered leaves. Besides being a three-dimensional model of motion with full degrees of freedom, this study improves the consideration of the motion of the vegetation in all directions, and in addition the energy and momentum transfer in the spanwise direction. Furthermore, we perform a flume experiment for the flow with submerged flexible vegetation, the results of which are used to validate the simulation effects of the numerical model. It is found that the numerical model can effectively simulate the velocity profiles and the movement of vegetation induced by the flow. Using the model to analyse the flow–vegetation interaction, we find that the movement of vegetation is closely related to the flow velocity. As the flow velocity increases, both the offset angle and the vegetation swaying amplitude increase. Compared to vertical rigid vegetation, the tilting of flexible vegetation does not significantly change the velocity difference and the magnitude of the turbulent kinetic energy between the inside and the outside of the vegetation canopy, but it does weaken the disturbance to flow, thus reducing the resistance to flow. However, the swaying of vegetation dose significantly increase the velocity difference between the inside and the outside of the canopy. It forms Kelvin–Helmholtz hairpin vortices intensifying the turbulence production, and enhancing the disturbance and resistance to flow.