The phase aberrations caused by thermal deformations is one of the main limitations in a beam control system. If left uncorrected, it would significantly reduce the effectiveness of high-power lasers as devices for beaming power over long paths through the atmosphere. For the purpose of overcoming the effects of phase aberrations, the method of conjugation wavefront pre-compensation of incident laser is introduced and theoretically studied. Based on the simulated results of thermal deformations at different irradiations time, choosing the power in the bucket (PIB), Strehl ratio, and the root-mean-square of phase as the characteristic parameters, the beam quality of emitted laser with and without wavefront pre-compensation is calculated respectively and compared. The result shows that under the condition that the conjugation compensation phase is placed on the incident beam, the beam quality of emitted laser is ameliorated prominently especially for a beam control system with serious thermal deformations.