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A numerical scheme to simulate three-dimensional two-way fluid–structure interaction (twFSI) problems of flows around a flexible fine structure is developed in this study. The partitioned approach is employed to separately calculate fluid flows and structure motions by the lattice Boltzmann method (LBM) and the geometrically exact Cosserat rod model (CRM), respectively. The fluid–structure interactions are calculated by the simple explicit coupling scheme combined with the contact detection algorithm and the fluid–structure interface reconstruction scheme. The contact detection algorithm utilizing the bounding volume hierarchy is adopted to reduce the computing time of data communication between the fluid and the structure solvers, while the fluid–structure interface reconstruction scheme utilizes the level set method to represent the moving fluid–structure interfaces. The proposed LBM–CRM–twFSI scheme is successfully validated in two experimental benchmarks of a single flexible structure deformation in a wind tunnel. The results confirm that the present scheme accurately calculates the equilibrium state and the time-dependent oscillatory motions of the structures exposed to airflows. The errors of the representative rod position between the experimental and numerical results for both benchmarks are within 5%. These validations confirm the practicability of the presently developed LBM–CRM–twFSI scheme for motions of flexible fine structures in fluid flows.