Computer-generated hologram (CGH) plays an important role in testing high-accuracy optical elements such as aspheric and freeform surfaces. However, the orthogonality error induced by the rails of direct laser writing systems will deteriorate the fabrication accuracy of CGH, and thus introduce astigmatism error to the testing results of surface shape. To quantitatively study the influence of orthogonality error induced by the rails of direct laser writing systems on testing results of CGH, a model of rails′ angle error of direct laser writing systems using scalar diffraction theory is established, and the impact of orthogonality error on the alignment section of the CGH is analyzed. The experimental results indicate that there is 2.26%, 2.33% and 1.72% deviation in root mean square(RMS), peak valley(PV) and Zernike astigmatic coefficient respectively with theoretical results when orthogonality error is 800 μrad, which verifies the correctness of the established error model.