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The amplitude of frequency spectrum can be integrated with probabilistic data association (PDA) to distinguish the target with clutter echoes, especially in low SNR underwater environment. A new target-tracking algorithm is presented which adopts the amplitude of frequency spectrum to improve target tracking in clutter. The probabilistic density distribution of frequency spectrum amplitude is analyzed. By simulation, the results show that the algorithm is superior to PDA. This approach enhances stability for the association probability and increases the performance of target tracking.