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Complementary sequences are well studied in the communication field for their good correlation properties. Besides being used as spreading sequences, they can also be used for channel estimation, synchronization, reduction of peak-to-average power ratio of symbols, preamble design, sequence design, Target detection and so on. A recursive construction of complementary sequences based on orthogonal matrix and permutation matrix is proposed, which increases the number of complementary sequences in the set by increasing the number of their sub-sequences with the same sequences' length. Then the anti-interference performance of multi-carrier CDMA (MCCDMA) system based on complementary sequences is simulated, and the obtained results show that it has better anti-interference ability than traditional CDMA system.