The noises affecting the performance of a repeaterless long-haul fiber hydrophone system are investigated. For the noise due to pre-amplifier, distributed Raman amplifier (DFRA) and erbium-doped fiber amplifier (EDFA) are combined to decrease the noise and the experimental results in noise reduction agree well with the simulated results. The suppression of double-Rayleigh-scattering (DRS) inducing coherent noise by employing the phase generated carrier (PGC) modulation/demodulation technique is demonstrated and the suppression of DRS in systems with different fiber lengths is also discussed. The experimental results show that PGC technique scheme can suppress the DRS noise by 19 dB and the DFRA/EDFA hybrid scheme can decrease the pre-amplifier noise by 7.2 dB. In the end, the phase noise level of a hydrophone system with 100 km long-haul fiber reduces to -113.2 dB (namely 2.2 μrad/Hz1/2), which is identical to the level of a short-haul system. In the system with 200 km fiber, the noise level decreases to -104 dB (namely 6.3 μrad/Hz1/2) and the little increase of the noise is mainly due to the DRS which has not been completely suppressed.