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Because of the hostile ocean transmission condition, underwater acoustic communication technology is one of the most difficulty communication technology. Frequency-Hopping underwater acoustic communication system is drawing more and more attention for its good performance under serious noise and multi-path interference condition. Synchronization signal processing is a key factor of FH underwater acoustic communication system. In the research of FH shallow underwater acoustic data communication system, a synchronization method employing adaptive line-spectrum enhancing (ALE) method, frequency diversity, pulse width judgment and frame synchronization signal correlation processing to detect synchronization signal under the condition of low SNR and heavy amplitude fluctuation is presented. The sea experiment results are satisfactory.