The power capture performance of an interconnected two-raft wave energy converter (WEC) is investigated in this paper. The equations of motion for the hinged WEC are established using a discrete-module-beam-bending based hydroelasticity method. A mathematical model is then derived for the optimization of power-take-off systems, which is capable of taking into account both different raft length ratios and structural flexibility levels. Based on this mathematical model, the combined effects of raft length ratios and structural flexibility on the power absorption of the hinged two-raft WEC are explored in detail. A small fore-aft raft length ratio is beneficial to power capture in relatively short waves and the performance is further enhanced by the increase of structural flexibility. For relatively long waves, two rafts of equal length may be the optimal condition while the energy absorption is weakened by the structural flexibility. The critical wave number (normalized by the length scale of the rafts) categorizes the effect of structural flexibility on power capture into constructive (larger wave number than the critical value) and destructive (smaller wave number) regions and it is not very sensitive to geometric features of the WEC such as the width of two rafts and the gap between them.