A method for manufacturing a compound refractive lens for focusing X-rays in two dimensions. The method includes the following steps: 1) manufacturing a mother lens; 2) manufacturing a daughter lens; and 3) assembling the mother lens and the daughter lens. The assembly of the mother lens and the daughter lens includes: aligning square embedded lens bodies of the daughter lens with square holes of the mother lens, respectively, for allowing the first parabola-shaped holes on the mother lens and the second parabola-shaped holes on the daughter lens to form an orthogonal structure; and inserting and pressing the square embedded lens bodies into the corresponding square holes, respectively. The method of the invention has advantages of high-precision for manufacturing and calibration of optical axis, and meanwhile the compound refractive lens manufactured based the method has high X-rays focusing efficiency.