As an important part of navigation and positioning system, high accurate clock synchronization has a direct bearing on the positioning accuracy of the system. A clock synchronization scheme based on entangled signal is proposed. The HOM interferometer is balanced by adjusting an optical delay unit, the time of arrival of simultaneously generated photons is recorded by Clock A and Clock B, and a correlation on the time of arrival is analyzed to determine the clock offset from Clock A and Clock B, ensuring that Clock A is synchronized with Clock B. This method is used to effectively eliminate effects of background noise and achieve high accurate clock synchronization.