In gravitational wave detectors, the laser is used to observe how the distance between mirrors changes due to space distortions caused by gravitational waves. The displacement of the mirrors is minute, so the mirrors must be sufficiently isolated from ground vibrations to achieve the required sensitivity. Therefore, in KAGRA, the gravitational wave detector in Japan, the main mirrors are suspended by nine-stage pendulums. In such a pendulum-based vibration isolator, the mirror oscillates significantly at the resonant frequency. Then we need the control system to suppress the vibration, but the noise from the sensors used in such a control system can be a problem. In fact, the sensitivity of KAGRA was limited by the noise from the cryogenic payload control system at 10-100 Hz in the previous observation. Therefore, a low-noise control filter was designed and implemented for use in the observation phase. As a result, the control noise of the cryogenic payload at 10-100 Hz was reduced by 2-3 orders of magnitude, and the target sensitivity for O4 observation was achieved at low frequency (below 100 Hz).