A new fractional-order multi-carrier M-ary differential chaos shift keying system with multilevel code-shifted modulation (MC-MDCSK-MCS) is presented in this paper. The proposed system adopts multiple subcarriers, on which multiple MCS-MDCSK-modulated signals are transmitted simultaneously. Moreover, M-ary modulation has been combined with the proposed system to achieve a higher bit rate. On the receiver side, the recovered reference signal is first averaged and then used for MCS-MDCSK demodulation, which helps improve performance. We analyze the bit error rate (BER) of the proposed system and verify our theoretical derivations with the simulation results over additive white Gaussian noise (AWGN) and Rayleigh fading channels. Finally, related comparisons are completed, which show that the MC-MDCSK-MCS system is excellent and promising.