Previous studies have introduced a resonant caisson designed to enhance wave energy extraction in regions with low wave energy density; however, its operational mechanism remains poorly understood. This paper seeks to elucidate the operational mechanism of the resonant caisson by leveraging Star-CCM+ for Computational Fluid Dynamics (CFD) simulations, focusing on the influence of guides and their dimensions on the water levels, flow velocities, and vortex dynamics. The findings demonstrate the remarkable wave-amplification capabilities of the resonant caisson, with the maximum amplification factor reaching 2.31 at the calculated frequency in the absence of guides. Incorporating guides and expanding their radii substantially elevate the flow rates, accelerate the water currents, and alter the vortex patterns, thereby further enhancing the amplification factor. This study will provide a reference for optimizing the design of resonant caissons and wave energy converters based on resonant caissons, thus promoting the effective use of wave energy resources.