The invention provides a method and device for synchronizing the frequencies of a PTP master clock and a slave clock, and relates to the technical field of frequency synchronizing. The method includes the steps of determining the measurement value of clock deviation between the PTP master clock and the PTP slave clock each time, conducting calculation through a Kalman filtering method according to the measurement value of the clock deviation, determining the estimation value of the clock deviation between the PTP master clock and the PTP slave clock each time, determining the frequency deviation of the PTP slave clock relative to the PTP master clock at the kth time according to the estimation value of the clock deviation at the kth time and the estimation value of the clock deviation at the (k-1)th time, converting the frequency deviation of the PTP slave clock relative to the PTP master clock at the kth time into a voltage signal through a digital-to-analog converter, outputting the voltage signal to the voltage control end of a voltage control crystal oscillator of the PTP slave clock so as to make the voltage control crystal oscillator of the PTP slave clock output a frequency signal to serve as the datum frequency of the PTP slave clock, and synchronizing the datum frequency and the frequency of the PTP master clock. By means of the method and device, the problem that in the prior art, the synchronization of the frequencies of the PTP master clock and the PTP slave clock is not accurate enough is solved.