To effectively extend physical layer key generation techniques to the underwater acoustic channel, a novel underwater key generation scheme is proposed. First, a local pilot auxiliary wait channel sounding protocol is proposed to solve impaired reciprocity problems caused by the great transmission delay. At the same time, the protocol ensures high key entropy and prevents the nearby eavesdroppers. Second, two traditional enhancing mechanisms are applied to improve the key agreement. Third, an assembly line protocol is proposed to solve the problem that the key generation rate decreases rapidly with the increase of communication distance. Fourth, a double-layer compensation centralized quantization combined with adaptive guard interval quantization method is proposed to improve the rate of key agreement and key generation. Finally, simulation results show that the bit error rate is lower than 0.01, and the key generation rate is higher than 600 bits/s, which verify the superiority of the proposed scheme.