Two-photon polymerization lithography is a technique that provides hundreds of nanometer resolution and full geometric freedom. Several X-ray polymer refractive lenses created by this technique were characterized using differential phase contrast imaging (DPCI) with a microfocus X-ray grating interferometer. The beam deflection angle and wavefront phase shift of the X-ray beam through the lens were obtained. Comparative tests using synchrotron radiation sources showed that the system could measure the surface shape of X-ray refractive lenses with an accuracy of 0.4 µm. This study is important for improving the fabrication process and focusing performance of X-ray refractive lenses.