A miniaturized underwater polarized radiation measuring instrument (MUPRMI) LiDAR system applied in detecting the polarization optical parameter profiles for shallow water has been designed. This system will be used for detecting the depolarization of laser propagating underwater. For that purpose, a 532 nm linearly polarized laser with the repetition rate of 100 Hz and per pulse of energy of 50 μJ will be used in the system. When propagating underwater, the polarization state of laser will be changed in case of collision with the particles suspended in water. The linearly polarized laser will gradually become non-polarized due to depolarization, and the depolarization degree is related to the suspended particles. In order to detect the depolarization effect of waters, two orthogonal polarization receiving channels have been assembled in the MUPRMI system. For signal receiving, a photomultiplier tube has been assembled in each of the channels. By detecting the change of polarization state, parameters of scattering particles suspended in water in the detecting area can be inverted using inversion algorithm. The MUPRMI system can be controlled by a host computer, which communicate with the MUPRMI system using ethernet communication protocol. An adjustable aperture driven by a stepping motor has been assembled in the receiving optical path. Using this adjustable diaphragm, we can control the change of receiving field of view by transmitting instructions from the host computer, and change the reception of signals from different kind waters. A ship-borne experiments have been conducted in South China Sea, results show that the deepest bathymetry of the MUPRMI system is about 9 meters with the pulse energy of 50 μJ, in South China Sea.