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Aiming at the timing synchronization problem in underwater acoustic single-carrier frequency domain equalization system (SC-FDE), the training sequence and new metric function is constructed by using the well-related Zadoff-Chu (ZC) sequence, and the genetic algorithm is used to optimize the combination structure, which solves the problems of peak platform and false peak interference in the commonly used synchronization methods. Simulation results show that the improved synchronization algorithm is more accurate at the timing point under low signal-to-noise ratio and has high synchronization accuracy.