As the confliction between two cognitive radio （CR） systems and the interference among authorized users may degrade the performance of CR systems, an anti-jamming system for CR based on fractional Fourier transform （FrFT） is proposed. In this system, Chirp signal whose energy concentrates in FrFF domain is used as the base-band signal of CR, and the original data are restored via the filtering in FrFT domain and some correlative calculations. Simulated results show that the proposed system can extract the energy of expected signals and effectively suppress muhipath interference and the interference of other cognitive users, and that, when the interference is a cosine signal, bit error rate of the proposed system is lower than that of the system without FrFT.