A cross layer authentication method based on radio frequency fingerprint, it includes the following steps: S1. In the first time slot, the legitimate transmitter A sends the first packet to the legitimate receiver B, and then B identifies the first data packet by the upper layer authentication; S2. The legitimate recipient B extracts the RF fingerprint eigenvector of the legitimate sender A, and stores it in the memory of the legitimate receiver B; S3. In the next time slot, the sender X sends the second packet to the legitimate receiver B, and the legitimate recipient B extracts the RF fingerprint eigenvector of the sender X; S4. Set sample of the RF fingerprint eigenvector; S5. legitimate receiver B estimates the similarity between the RF fingerprint eigenvector of the sender X and sample of the RF fingerprint eigenvector. This invention is in advantage of low computational complexity, small delay and high precision.