The invention discloses a pilot-tone signal transmission method and a system thereof. The method includes that at transmitting end, converting physical characteristics of an original pilot-tone signal, and then transmitting the converted pilot-tone signal on an optical fiber; at receiving end, anti-converting physical characteristics of the pilot-tone signal extracted from the optical fiber to recover to the said original pilot-tone signal. The system includes a source device, a target device, an electro-optical converter, optical fibers, an optic-electronic converter, a signal-extracting device, a signal-converting device and a signal-anti-converting device. With the above technical scheme, the invention overcomes carrier/noise ratio limitation, provides better SN ratio performance, and can effectively recover the pilot-tone signal to its original form even the SN ratio condition is worse.