A method based on the diffraction theory for estimating the three-dimensional (3D) focusing performance of the compound refractive X-ray lenses is presented in this paper. As a special application, the 3D X-ray intensity distribution near the focus is derived for a plano-concave compound refractive X-ray lens. Moreover, the computer codes are developed and some results of 3D focusing performance for a compound refractive X-ray lens with Si material are shown and discussed.