In this letter, a novel physical layer encryption method based on digital chaos is proposed for the security in high-speed intensity modulation and direct detection (IM/DD) discrete multi-tone (DMT) transmission system. In the proposed encryption scheme, a random interleaving method is used, which further enhances the ability to encrypt the quadrature amplitude modulation (QAM) constellation and improves the transmission performance. In addition, probabilistic shaping (PS) technique is also cascaded into the encrypted transmission system for the first time. Adopting the proposed algorithm, we experimentally demonstrated the transmission of 100-Gbit/s encrypted 64QAM and PS-64QAM DMT signals over 2-km standard single-mode fiber (SSMF).