A clock calibration method of a navigation system is provided. The clock calibration method includes: entering a calibration mode; sequentially issuing, by a host, a count start signal and a count end signal separated by a time interval; counting a local oscillation frequency of a local oscillator when a navigation device receives the count start signal from the host; disabling the counting when the navigation device receives the count end signal from the host and generating a current count; generating a calibration signal according to the current count and a predetermined count corresponding to the time interval; and calibrating the local oscillation frequency of the local oscillator according to the calibration signal.