The hydrolocation noise measurement system integrated with the buoy and subsurface buoy can realize the all-weather noise measurement of targets with different noise radiation levels in the monitoring water area. The addition of high-precision clock and GPS ensures that the system can accurately predict the motion trajectory of underwater targets at each time. In order to ensure the system accuracy when measuring the noise, the frequency spectrum compensation correction algorithm is used so as to improve the precision of time-delay calculation remarkably. The main control software of system can display the trajectory of target to be measured, process the underwater target noise by integrating the time, position, acoustic measurement information, etc., and obtain the noise power spectral density and other characteristics. The results of lake tests show that the positioning result of system is stable and reliable.