In a high-power laser system, a beam splitter refers to the mirror which locates at the cross point of the path of highpower beam and the weak light section. Because of the thermo-optic effect and elasto-optic effect, a beam splitter deforms under intense laser radiation. This deformation adds extra phase on the incident waves and deliveries inaccurate information to the wavefront sensor. Consequently, the output laser focuses at finite distance and gets divergent when arrives at the target. To settle the above problem, this paper presents a new method for real-time correction of the thermal distortion of beam splitter, based on algorithm of the data fusion of two Shack-Hartmann wavefront sensors (SH-WFS). Different from the traditional AO system, which contains a wavefront sensor, a corrector and a servo controller, two extra Shack-Hartmann wavefront detectors are adopted in our AO system, to detect the transmitted and reflected aberrations of beam splitter mirror. And these aberrations are real-timely delivered to the wavefront sensor. Based on coordinate conversion and data fusion algorithm, it makes the wavefront sensor of AO can “see” the aberrations of splitter mirror by itself. Thus, the servo system controls the corrector to compensate these aberrations correctly. In this paper, the theoretical model of data fusion algorithm is carried out. A closed-loop AO system, which consists of a typical AO system and two extra Shack-Hartmann wavefront detectors, is set up to validate the data fusion algorithm. Experimental results show that, the distortion of a CaF2 beam splitter can be real-time corrected when the AO closedloop control is on. The beam quality factor of output laser decreases from 4 to 1.7 times of diffraction limit.