We proposed an efficient and low-cost method for precise fabrication of large-area microstructures. A programmable digital lithography system based on digital micromirror device (DMD) oblique scanning strategy was developed, which can effectively reduce pixel quantization errors and complete a sub-pixel exposure accuracy. To further reduce the cost and enhance the flexibility of the fabrication system, a two-dimensional (2D) stage self-calibration technique is studied, which can replace the laser interferometer measurement (LIM) system and ensure the calibration accuracy well. The presented method is promising for developing large-area microstructure applications such as flat panel display (FPD), organic light-emitting diodes (OLED).