As the combination of OFDM and CDMA, MC-DS-CDMA is a strong candidate for future wireless communication. However, challenges remain before it can achieve full potential. In this paper, we concentrated on reducing the peak-to-average power ratio (PAPR) in MC-DS-CDMA system and proposed an effective method, which takes advantage of the characteristics of MC-DS-CDMA system. At transmitter, chips after time spreading are pseudo-random permuted firstly and clipping is exploited to reduce the PAPR. At receiver, the order of chips is recovered and the clipping noise is estimated and canceled. As a result, signal PAPR can be effectively controlled by clipping while avoid being severely distorted at some certain points by chip pseudo-random permutation at transmitter, and system performance loss caused by clipping can be mitigated to very little by canceling the clipping noise at receiver