The invention discloses a nuclear reactor cooling pump vibration phase signal acquisition method and a system thereof, which belong to the technical field of nuclear power station safety. The system comprises a vibration probe, a vibration signal processor, a phase probe, a reference pulse signal processor, and a phase signal processor; the vibration probe is electrically connected with the vibration signal processor, the phase probe is electrically connected with the reference pulse signal processor, and the vibration signal processor and the reference pulse signal processor are connected with the phase signal processor in a communication mode. A reference pulse signal can be obtained by the newly added phase probe, the obtained reference pulse signal and a current vibration signal are calculated according to the phase signal processor, a vibration phase signal of a main shaft of a cooling pump of a nuclear reactor can be obtained, the vibration phase signal of the main shaft of the cooling pump of the nuclear reactor can be monitored through acquisition of the vibration phase signal of the cooling pump of the nuclear reactor, and furthermore, the vibration condition of the cooling pump of the nuclear reactor can be comprehensively analyzed.