The invention discloses a frequency domain weighting phase comparison method for X-ray pulsar photon sequences and solves the problems that in the prior art, detailed information of a useful signal is lost, calculation complexity is high, and the signal to noise ratio is low. The method comprises the following steps: 1, conducting evenly-spaced sampling on two photon arrival time sequences received by two spacecrafts, and obtaining corresponding photon intensity sequences; 2, converting the two photon intensity sequences in a time domain into a frequency domain through an FFT; 3, extracting phase information of the two photon intensity sequences, conducting subtraction arithmetic, and obtaining phase differences between the two photon intensity sequences; 4, accumulating the phase differences which are sectionalized, and extracting ratios of the phase differences to corresponding frequency points; 5, conducting energy weighting and proportional multiplication on the ratios of the phase differences to frequency in the frequency domain, and obtaining a normalized delay phase within the time domain. By means of the frequency domain weighting phase comparison method, phase estimation accuracy can be effectively improved, calculation complexity can be lowered, and the method can be applied to estimation of the relative movement state of an X-ray pulsar relative to a navigational positioning system.