The MC-DS-CDMA system, OFDM technology is applied in, has some good properties, such as high-speed transmission and restraining multi-path interference. However it has some shortcomings. Lots of resource of frequency is used in this system. Because traditional spreading spectral sequence doesn’t have good property of auto-correlation and cross-correlation in the meantime, it leads to multi-access interference. In this paper, a new communication system of MC-DS-CDMA system using modified complementary sequences as spreading spectral sequence will be proposed to solve those problems. Based on the theory of complementary sequences and OND, the concept of dummy chip is led in. According to the algorithm of dummy chips generation, the whole frame data will be processed and becomes the extended frame which is also called modified complementary sequence. The dummy chips in the extended frame become an undisturbed window. When received data is carried on the particular correlating computation of complementary sequence in the undisturbed window, the primitive transmitted data will be restored correctly. The performance of MC-DS-CDMA system based on modified complementary sequence has been analyzed and simulated. The result of simulation proved that this measure is proper and feasible. With the quotation of this technology, the system can efficiently eliminate multi-path interference and decrease multi-access interference to a low level under the condition of using less subcarriers relatively.