Consistent with the scanning structure of airborne laser bathymetry system, aiming at the oval scanning mode of circular mirror skew axis, starting from the beam emission direction and on basis of the axial relation of scanning structure, the laser output direction vector was derived by the law of light reflection. The coordinates of laser points on the sea surface were obtained by combining the distance from the laser output location to the sea surface point. According to the law of light refraction, the coordinate calculation formula of submarine bathymetric point was derived by using the variable refractive index ray tracing algorithm, and the precise calculation model of laser incident point and submarine bathymetry point coordinate was established. According to the model positioning formula, the influence of scanning system boresight error was analyzed. Through numerical simulation, the influence of scanning boresight misalignment calibration on positioning accuracy was analyzed, which provided the basis for the processing, installation, adjustment and the integrated checking of unit device in the scanning system. The positioning formula can provide reference for accurate calculation and correction of submarine points for airborne lidar bathymetry system.