In this study, an alternative way, a so called caisson based type of oscillating water column (OWC) wave energy converting system was proposed to capture and convert wave energy. Since the caisson structure is constructed to protect the coastal line or ports, it is important to know if a built-in associated OWC system will be a burden to affect the safety of the structure or it is safe enough to work appropriately. In this study, three steps of structural analysis were performed: firstly, the analysis for the structural safety of the whole caisson structure; secondly, performing the mechanic analysis for the chamber of the associated OWC system; and finally, performing the analysis for the wave induced air-pressure in the chamber under the design conditions of a local location during the wave-converting operation. For the structural safety analysis, a typical structural model associated with caisson breakwater was built and analyzed while the shape of the structure, material applied to the construction, and associated boundary conditions were all set-up according to the wave and structures. The motion and the strain distribution of the caisson structure subjected to designated waves of 50-year return period were evaluated and compared to the safety requirement by the code. For the analysis of the energy converting performance, a numerical method by using a theorem of unsteady Navier–Stokes equations in conservation form was used to analyze the proposed OWC model when the structure subjected to an incident wave of a 10-year return period.