The invention discloses a deepwater underwater positioning system, which comprises an underwater platform measuring position indication subsystem (2) which can set a master/slave relationship and a water platform control tracking subsystem (1) which corresponds to the underwater platform measuring position indication subsystem (2); and the underwater platform measuring position indication subsystem (2) comprises a hemispherical direction measuring position indication transduction unit (9) capable of receiving and transmitting an acoustic signal and a measuring position indication management unit (10) for distinguishing a position indication working mode or a measuring working mode in the acoustic signal and processing the acoustic signal, and the water platform control tracking subsystem (1) comprises a multi-elementary acoustic measuring matrix for receiving and transmitting the acoustic signal and a control tracking management unit (4) for processing the acoustic signal. The deepwater underwater positioning system has various working modes, and is capable of integrating flexibility and precision and wide in application range.