Aiming at the impact of underwater noise uncertainty on information transmission and the security problems faced by communications in noise channels, a secure communication scheme based on the uncertainty of underwater noise channels is proposed. The scheme consists of an interactive key extraction protocol based on Godel coding and a confidentiality enhancement protocol based on r−cyclic Toeplitz matrix. In the process of key extraction, Godel coding is introduced to reduce the number of comparisons of key sequences; when calculating the secret-enhanced key length, the uncertainty of underwater noise is considered, which has stronger practical significance. The experimental results show that under the condition of meeting the security of the protocol, the total number of bits transmitted is 119940 bits, the lower bound of the total length of the key string generated after confidentiality enhancement is 117331 bits, and the upper bound of the amount of information about the key string by the adversary It is 2609 bits, the required time is 11.99s, and the proposed (nt+s)×(nt+s)order r-cyclic Toeplitz matrix reduces the storage space of (nt+s)-1 bit compared with the traditional Toeplitz matrix of the same order.