Non-continuous orthogonal frequency division multiplexing (NC_OFDM) has large sidelobe power and high peak-to-average power ratio (PAPR).In this paper, an improved algorithm with Fountain coding was proposed, in which the sidelobe interference in NC-OFDM system and high peak to average ratio were both taken into consideration in the joint optimization algorithm under the circumstance of cognitive radio system.Fountain multi-choice sequence algorithm, by the ideal of Fountain coding and sequence mapping, was adopted for sidelobe suppression and PAPR reduction.The simulation results show that the improved algorithm can significantly reduce the band interference to licensed user (LUs) and make the system PAPR less than target PAPR, so as to solve the problem of NC_OFDM signal distortion caused by power amplifier and eventually enhance the performance of the bit error rate effectively.