For the spatial periodic modulation that affects the output performance of high power laser systems, a novel method of compensating and controlling the spatial periodic modulation based on phase carrier is proposed and analyzed. First, the theoretical analysis shows that this method is able to control the spatial frequency of the spatial periodic modulation. The intensity of the spatial frequency is modulated by changing the magnitude of the phase carrier, and for the amplitude-type spatial periodic modulation, the period of the phase carrier can change the position of the maximum intensity of the spatial frequency. Then, the experiment on the effect of phase carrier on the amplitude-type spatial periodic modulation is carried out. The feasibility of the method is verified by experimental results and numerical simulations. The output near-field beam and the corresponding one-dimensional average power spectral density curve before and after the phase carrier modulation are compared. It is found that the peak value of the spatial frequency drops by an order of magnitude and decreases to near the background value after phase carrier modulation in the experiment. This method provides a new way to compensate and control the sensitive spatial periodic modulation in high power laser systems.