Due to the limitation of laser pulse width, traditional lidar cannot achieve shallow water measurement of tens of centimeters. A polarization lidar with dual Geiger-mode avalanche photodiodes (Gm-APD) was designed to achieve high-precision depth image of shallow water layer by using a wide laser pulse. The surface of the shallow water layer was smooth and had good polarization-maintaining characteristics, whereas the bottom surface was rough and had certain depolarization characteristics. According to this feature, by emitting horizontal linearly polarized light, a polarization beam splitting prism was used in the receiving system to separate the front and rear surface signal lights, and then they were detected by two Gm-APDs respectively. The system was not limited by the pulse width of signal light, and made full use of the dead time mechanism of Gm-APD to realize the depth measurement of ultra-thin shallow water. Using the principle of polarization transmission of the Stokes parameter and Muller matrix, the principle of light splitting of the dual Gm-APD polarization lidar was theoretically analyzed. Signal restoration & center-of-mass algorithm method was used to restrain the range walk error to obtain high range precision. The thin shallow water layer had a gradient from 4.5 cm to 8 cm in depth, and the bottom surface of which was covered with black and white sand. In the experiment, a 6 ns width laser pulse was used to obtain a high-precision depth image of the thin shallow water layer at the detection distance of 5 m with the accuracy of 0.8 cm. This effectively verifies the feasibility of the scheme. This scheme can provide certain reference for the measurement of shallow ocean water layer in in airborne lidar bathymetry systems.