The invention relates to a system and method for locking phase and tracing the time synchronization, the said system includes: the receiver of clock source which is used to receive the second impulse signal and state data of clock source; control device for clock phase-lock which is connected with the receiver of clock source, read the state data of clock source and analyses it to choose a route to trace the second impulse signal, and the traced signal is output according to the need of user. Said method includes: a. receiving the second impulse signal from the clock source and state data; b. analyzing the state data of clock source, and according to the analyzed result choose the second impulse signal; c. tracing the second impulse signal by locking phase and output the signal according to need frequence of user. To solve the problem that caused by using the receiving unit of ''Dipper No. 1'' need to provide local parameters which is lack by hand; and at the same time, it solves the unreliable problem that caused by using the GPS as the clock synchronizing system of synchronizing source.