Floating breakwaters (FBs) have been attracting attention as wave safeguards due to the low construction cost and fast installation, but their wave attenuations are sensitive to structural configuration. Horizontal flanges have been proven sufficient in improving the wave attenuation of restrained box FB, but how it evolves in the moored FB has not been understood. This paper focused on the configuration of horizontal flanges, including the installation position, immersion depth, flange length, and asymmetry of flanges on the hydrodynamic performance of moored box-type FB under regular and irregular waves. A CFD numerical flume was developed through a grid convergence test and validated with experimental results. A novel parametric study in flange configuration was conducted, exploring the law of the flange configuration versus the wave attenuation, floater motion, and mooring tension. The results indicate that the flanges can improve wave attenuation and reduce motion response but increase the mooring tensions. The horizontal flanges enlarge the blockage area to water particles and concentrate the vortices closer to the flanges, increasing the reflection and improving wave energy dissipation. The box-type FB can be enhanced by installing flanges higher and offset toward the offshore side, which provides suggestions for the flanges’ design.