Aiming at the problem of secure communication in physical layer of optical network, a coherent communication quantum noise stream encryption(QNSC) system scheme based on low density parity check(LDPC) code is proposed. The LDPC code with a bit rate of 9/10 and discrete Fourier transform orthogonal frequency division multiplexing(DFT-OFDM) technology are applied in the system scheme. Finally, the scheme is verified by experiments. The experimental results show that after transmitting the standard single-mode fiber with the span of 40 km, 80 km, 120 km and 160 km, The LDPC code effectively reduces the bit error rate of the system, improves the communication security of the system, and does not affect the basic performance of the system.