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Two-photon polymerization (TPP) has recently been applied to produce affordable refractive 3D microlenses for focusing hard X-rays and X-ray full-field microscopy. To achieve diffraction-limited focusing, the lens working surface should be precisely parabolic. During TPP, the structure is being printed voxel by voxel, and the voxel is shaped as a prolate ellipsoid stretched along the optical axis with a sub-micrometer size at best. Considering this, the ideal computer model printed by ellipsoidal voxel deviates from parabolic shape, which leads to aberrations when focusing X-rays. For example, an optical system of 30 individual lenses demonstrated a sagittal focus of 45 mm and tangential focus of 37 mm when using 12.7 keV photons. Here, we propose a method for pre-correcting the computer model considering the voxel shape, reducing the deviation of the printed lens from the parabolic shape. We have printed the lens models from IP-Dip photopolymer by Nanoscribe Photonic Professional (objective lens 63x/NA1.4) with constant laser power of 9 mW, corresponding to the voxel’s major and minor axes of 300 nm and 600 nm, respectively. We successfully test the method by printing X-ray microlenses with a 2-10 um curvature radius and an optical axis parallel to the substrate surface. We compared the lenses’ curvature radii and apertures determined from SEM images of cross-sections of printed corrected and uncorrected lenses. The research can advance the production of high-quality X-ray optics by TPP.