To improve the robustness of the communication system in complex underwater acoustic environment, the hybrid carrier system based on WFRFT was put forward. To obtain the optimal transformation order, the hybrid carrier system is designed with the lowest bit error rate as optimization goal. Simulation results show that BER performance of hybrid carrier system is between the traditional single/multi carrier systems in multipath channels. However, system performances with the optimal order are superior to single/multi carrier systems under the doubly selective fading channels. It has the excellent characteristics of the single/multi carrier systems and it is thus prospective in improving the robustness of the communication system.