A single wavelength(532 nm), short-pulse(400 ps), low pulse energy(0.5 μJ), high pulse repetition rate(10 kHz), short dead time of detector(22 ns) and high resolution of time interval(50 ps) photon counting laser bathymetry system was designed. The principle of photon counting laser bathymetry and its superiority to the typical airborne laser bathymetry was introduced. The relationship between the average number of photoelectrons generated at the receiver and the transmitted laser pulse energy was analyzed, indicating that the bathymetry capability of the system was about 3.7 m. Experiments were conducted in a pond with a Secchi depth of 1.2 meters, and the underwater information down to 2 m depths were successfully obtained by filtering and solving the point cloud data.