The multi-dithering method has been well verified in phase locking of polarization coherent combination experiment. However, it is hard to apply to low repetition frequency pulsed lasers, since there exists an overlap frequency domain between pulse laser and the amplitude phase noise and traditional filters cannot effectively separate phase noise. Aiming to solve the problem in this paper, we propose a novel method of pulse noise detection, identification, and filtering based on the autocorrelation characteristics between noise signals. In the proposed algorithm, a self-designed window algorithm is used to identify the pulse, and then the pulse signal group in the window is replaced by interpolation, which effectively filter the pulse signal doped in the phase noise within 0.1 ms. After filtering the pulses in the phase noise, the phase difference of two pulsed beams (10 kHz) is successfully compensated to zero in 1 ms, and the coherent combination of closed-loop phase lock is realized. At the same time, the phase correction times are few, the phase lock effect is stable, and the final light intensity increases to the ideal value (0.9 Imax).