, Tae FMT(Filtered Multi-Tone) to Underwater acoustic communication(UAC) system are actively under way as UAC is utilized in the various fields and the demand of high speed data transmission increases. In the existing OFDM method, the use of virtual carrier, which is inserted not to affect the adjacent channel in the frequency domain, and the cyclic prefix, which is used to reduce the impact of Inter Symbol Interference and Inter Channel Interference, decrease the throughput. In particular, the length of cyclic prefix to be used becomes longer under water since underwater has a rapidly changing channel characteristic, and the data throughput diminishes because it has to allocate more subcarrier on virtual carrier. This study therefore suggests FMT-OFDM system, a combination of OFDM and FMT, for the purpose of enhanced throughput in the underwater channel environment. Besides, in this study, channel is modeled based on data measured in real sea and the performance is analyzed after setting system parameters.