In phase generation carrier demodulation of fiber laser hydrophone, the physical mechanism of inherent noise near 3 kHz is analyzed theoretically and proved by an experiment. The relaxation oscillation peak of pump laser is measured firstly, and the carrier signal frequency is gradually reduced at an interval of 400 Hz to observe the movement direction and magnitude of the inherent noise peak. The experimental results show that with the decrease of the carrier signal, the inherent noise peak moves to the low frequency direction, and the movement interval is also 400 Hz. Therefore, it is considered that carrier signal superimposed with the relaxation oscillation noise of pump laser is the cause of the inherent noise. Finally, the inherent noise is suppressed and a relatively flat background noise spectrum is obtained through reducing the carrier signal frequency of phase generation carrier demodulation algorithm.