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A long PN code sequence estimation and synchronization algorithm by subsection technique is proposed in this paper. Making use of the separability of response vector h(t) , estimation and synchronization of PN sequence can be made within each subsection. Then the recovery of the whole long sequence can also be simply reconstructed. What need to be dealt with are those smaller dimension blocked matrixes only, and computational complexity is largely reduced. Computational analysis shows that the subsection technique for long PN code sequence estimation does not lose the precision and SNR tolerance at all.