In this paper, the hydrodynamic performance of the comb-type breakwater-wave energy converter (CTB-WEC) system with a flange was investigated. Based on the linear potential flow theory, a semi-analytical model for wave interaction with the CTB-WEC system equipped with the flange was developed using matching eigenfunction method. In particular, Chebyshev polynomial was adopted to handle the singularity of velocity at the flange edge. Successful validation of the semi-analytical model was achieved by theoretical examination and comparing with the experimental data. The influence of wave resonance behavior in the confined water region (surrounded by caissons and the flange) was emphasized. It was found that: 1) the wave resonance behavior in the confined water region is modified due to the presence of the flange; 2) the hydrodynamic efficiency and wave attenuation performance of the CTB-WEC system is improved by properly configuring the flange; 3) the presence of piston and sloshing mode wave resonance in the gap between the WEC device and the flange led to the increment of hydrodynamic efficiency.