Optical homogeneity of the fused silica directly affects the wave-front quality of the optical system. Furthermore, three-dimensional optical homogeneity is required in order to produce high-precision prisms, because of its special optical demand. However, the three-dimensional optical homogeneity of fused silica is poor owing to the periodically grow laws based on vertical CVD technical in the process of ingots production. One circular and one square sample were prepared to measuring the three-dimensional optical homogeneity, founding that the vertical direction had worse optical homogeneity result compared to the horizontal direction. The constituents of the sample were tested and analyzed to found the inhomogeneity reason. The method was proposed to improve the three-dimensional optical homogeneity.