The present invention relates to the field of quantum communications, and provides a clock synchronization system and method. A clock synchronization system, comprising a signal sensing end and a signal receiving end. The signal sending end comprises a first laser pulse generator, a second laser pulse generator and an optical coupling module; the signal receiving end comprises a separation module, a photovoltaic conversion module and an optical detection module; and the signal receiving end is used for receiving a coupled optical signal, and separating, detecting and analyzing the coupled optical signal according to a wavelength difference of the coupled optical signal. In the present invention, laser of different wavelengths are coupled to a signal receiving end by an optical coupling module in a signal sending end, and an optical separation module separates the coupled optical signal according to a wavelength difference by means of the detection and processing of an optical detection module. It is ensured that a time reference is not affected by an optical path difference, simplifying the design complexity in electronics and supporting software, and avoiding impact on a system time resolution brought about by the optical path change of the receiving end.