When airborne lidar is detecting the underwater target, the laser beam will be influenced by the wavy sea surface. Based on Monte Carlo method, the space distribution of photons on the target surface is quantitatively analysed and the space distribution and time distribution of the photons return which the sea-air interface are analysed. Simulation results show that the space distribution of photons at the target surface gradually deviates from Gauss distribution as the velocity of wind increases and the space distribution badly of the photons which return the sea-air interface deviates from Gauss distribution. The influence of wind velocity is no longer important. By computing the time distribution of photons which return the sea-air interface, it is found that when the wind velocity increases, the detection depth of lidar decreases.