The present invention discloses a method and apparatus for aligning the phases of a master clock and a slave clock; and the method comprises the following steps: A. locking a phase of a master clock; B. measuring phase difference between a slave clock and the master clock; and C. adjusting a phase output by the slave clock so as to align it with the phase of the master clock based on the phase difference measured in Step B. The present invention also discloses an apparatus for aligning the phases of a master clock and a slave clock. By measuring the phase difference between the master clock and the slave clock, and aligning the phases of the master clock and the slave clock according to the phase difference the present invention improves the precision of phase alignment without increasing costs.