Aiming at the characteristics of the unmanned ship data link SC-FDE burst signal communication time slot change, a carrier synchronization method based on variable frame length and frame structure is studied. The autocorrelation function of the preamble sequence and the unique word (UW) sequence in the frame structure is used to complete the carrier synchronization. By designing the optimal differential correlation length, it provides sufficient frequency offset estimation range and higher estimation accuracy, while reducing the carrier computational complexity of the synchronization method. Finally, the performance of the designed carrier synchronization method is simulated in terms of frequency offset estimation range, frequency offset estimation accuracy and differential correlation length.