An automatic polarization compensation method for low-repetition frequency short optical pulse is proposed and successfully applied to the master oscillator room (MOR) in inertial confinement fusion (ICF) systems to maintain the MOR maximum output energy. After an average of 37 shots, the MOR output energy reaches maximum value with the sudden occurrence of polarization variation in the fibers. The peak-to-peak amplitude jitter of the MOR output is 9.52% at 4 h, which meets the requirement of the ICF system.