The invention discloses a kind of underwater GPS allocation and navigation system and method without high stable frequency scale. The system is made up of GPS satellite constellation, four or more GPS floating marks, underwater navigation transceiver, data control centre, sea level wireless communication loop and hydroacoustics communication loop. The method is: when the object underwater needed to be located, the underwater navigation transceiver sends out hydroacoustics localization signal to the GPS floating mark, the floating mark transmits the hydroacoustics localization signal, the GPS signal and the posture calibration data wirelessly to the data control centre, and the data are processed with the difference signal, works out the position and time sending out the localization signal of the underwater object, the position and time data are transmitted to the underwater navigation transceiver by the hydroacoustics communication system, it can carry on navigation or time service. The invention can be applied to underwater object tracing, underwater localization and navigation, underwater precise timer service, measuring project control and project structure sample, it needs no high stable frequency scale.