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An effective algorithm is proposed to estimate the spread spectrum sequence in direct spread spectrum sequence (DSSS) signal with the non-stationary noise for the underwater acoustic non-cooperative communication system. Conventional estimators are generally ineffective in detecting signals under low signal-to-noise ratio (SNR). The estimator proposed in this paper only needs the demodulation for the intercepted data sequence and time synchronization in advance. The first step is to realize the synchronization of the sequence by comparing different position values of the received signals. The second step is to estimate the direct spread spectrum sequence with the preprocessed data sequence after all the synchronizations have been accomplished derived separately. Computer simulation results show the blind estimator has reliable performance under different SNRs.