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Fluid-particle systems are very common in many natural processes and engineering applications. However, accurately and efficiently modelling fluid-particle systems with complex particle shapes is still a challenging task. Here, we present a numerical model that combines the advantages of Lattice Boltzmann Method (LBM) in solving complex flow problems and the capability of the recently introduced Metaball Discrete Element Method (MDEM) in handling non-spherical particle shapes. A sharp interface coupling scheme is developed and the numerical instability issues due to the discontinuity of interfaces are carefully addressed. A local refilling algorithm for new fluid nodes is proposed and special treatments are introduced to reduce numerical noises when two particles are close. The proposed model is validated by simulations of settling of a single sphere (with metaball representation) as well as a non-spherical particle in a viscous fluid. Good agreements are found comparing the simulations with experimental results which are also carried out in this study. The coupling scheme is also tested by multiple particle simulations which clearly illustrated the stability of the proposed model. Finally, numerical examples with complex particle shapes demonstrated that the proposed model can be a powerful tool for future applications such as shape-induced segregation in riverbeds, and phase transition of dense suspension.