We propose a hybrid automatic repeat request (HARQ) message combining method for frequency division duplex (FDD)-based flexible duplex systems. Utilizing a link condition between the base station (BS) and the user equipment (UE) while combining HARQ messages can reduce the throughput performance degradation caused by HARQ message bundling, which is necessary when the number of HARQ messages exceeds that of resources to report them. We analyze the average throughput performance according to the number of HARQ messages associated with multiple HARQ feedback bits and propose an algorithm to obtain an optimal solution. Moreover, we show the superiority of the proposed algorithm by evaluating the average throughput performance and the computational complexity.