Two-dimensional (2D) gratings are the key elements of optical encoders in lithography machines. Herein, an ultra-precision laser direct writing system is proposed. Based on the ultra-precision platform, we obtain a 2D grating mask with grid line density of 1200 line/mm after double exposure by rotating the substrate by 90°. The atomic force microscopy and scanning electron microscopy images indicate that the profile of the 2D grating mask is clear and its spatial uniformity is excellent. These results demonstrate that the proposed ultra-precision laser direct writing system effectively fabricates a 2D grating mask, showing promise in the fabrication of large, high-precision 2D metrological gratings.