Aiming at the problem of low data transmission security of visible light communication(VLC) link, the data transmission security problem of VLC link is becoming more and more prominent. In orthogonal frequency division multiplexing(OFDM) VLC system, a three-level physical layer encryption scheme with specific level, symbol level and phase joint encryption is proposed. Firstly, the chaotic sequence encryption method of Logistic mapping is introduced to reduce the correlation of encrypted data, improve the security of encrypted data and the transmission performance of the system. Then, the constellation mapping based on S replacement table is proposed, and the corresponding constellation mapping relationship is generated according to different S replacement tables, so that the characteristics of gray mapping are always maintained between the original binary bit data and the digital modulation signal generated after encryption, and the gray gain is guaranteed. The simulation results show that compared with the existing schemes, the proposed physical layer encryption scheme not only has higher security, but also reduces the pek-per-power ratio of the data sent by the OFDM VLC system, alleviates the nonlinear distortion generated by the light-emitting diode(LED) transmitter, and improves the bit error rate performance of the system.