Synchronization is very important in underwater acoustic OFDM communication system based on the fractional Fourier transform (FRFT-OFDM). To improve the synchronization performance, a new way is proposed in this paper, which use symmetrical triangular linear frequency modulation (STLFM) signal as the preamble for the system. A scheme of the communication system based on FRFT-OFDM is given in this paper. The synchronization algorithm using STLFM signal as the preamble is discussed in detail. Theoretical analysis and simulation results show that the proposed synchronization method in optimal fractional Fourier domain can significantly improve the synchronization performance of system as compared to the traditional method.