The immersed boundary method (IBM) has been popular in simulating fluid structure interaction (FSI) problems involving flexible structures, and the recent introduction of the lattice Boltzmann method (LBM) into the IBM makes the method more versatile. In order to test the coupling characteristics of the IBM with the multiple-relaxation-time LBM (MRT-LBM), the three-dimensional (3D) balloon dynamics, including inflation, release and breach processes, are simulated. In this paper, some key issues in the coupling scheme, including the discretization of 3D boundary surfaces, the calculation of boundary force density, and the introduction of external force into the LBM, are described. The good volume conservation and pressure retention properties are verified by two 3D cases. Finally, the three FSI processes of a 3D balloon dynamics are simulated. The large boundary deformation and oscillation, obvious elastic wave propagation, sudden stress release at free edge, and recoil phenomena are all observed. It is evident that the coupling scheme of the IBM and MRT-LBM can handle complicated 3D FSI problems involving large deformation and large pressure gradients with very good accuracy and stability.