Quantum communication is brand new way of communication in which quantum entanglement is used to transmit information. It is an interdisciplinary subject combining quantum informatics with modern communication theory. Motivated by the communication requirements for underwater sensor networks, submarines, etc., underwater optical communication has been developing rapidly in recent years due to the ideal information security of quantum communication. However, the research on the performance of underwater quantum communication in sea has not yet been fully developed because of a series of factors such as surge, salinity and seaweed and so on. In this paper, the influence of surge in non-uniform water flow on the underwater quantum communication is studied theoretically and experimentally. Firstly, a new Boussinesq equation with a given flow function is derived based on the horizontal and vertical wave velocity of the free surface to represent the free surface boundary conditions. On the other hand, In view of the nonlinear motion of movement, the complexity of change and the randomness of the distribution, the spectrum is used for numerically calculating the surge. The characteristics of wave motion are described by wave height, period and wavelength. Secondly, the influence of surge on the entanglement of underwater quantum channel is analyzed. It is proved that the wave height of surge and the change of the cycle affect quantum communication due to the destruction of the quantum coherence and the reduction in quantum entanglement degree. Thirdly, the influence of surge motion on the quantum channel capacity is studied. The influence of the relation between the wavelength and the transmission cycle on the quantum channel capacity is simulated. The relationship between the physical characteristics of surge wave and the capacity of depolarized channel is established. Fourthly, the influence of surge motion on error rate in quantum key distribution is studied. The simulation results show that when the sea surface wind speed changes in a range of 0-20.5 m/s, the propagation cycle is increased gradually. The channel entanglement is increased from 0.0012 to 0.8426, and the channel capacity is reduced from 0.8736 to 0.1024. In the key distribution process, the quantum bit error rate increases from 0.1651 to 0.4812. Therefore, in underwater quantum communication, the parameters of the system should be adjusted adaptively according to the varying degree of the surge movement.