We report a flexible and efficient method to pattern two-dimensional (2D) multi-scale structures by digital-mask projective lithography (DMPL) with an alterable projective scaling system. In the developed DMPL system, femtosecond laser was modulated by digital micromirror device (DMD) to generate a designable intensity distribution with digital image information. The projective law of this DMPL system based on the geometric optics theory verified for different projective scaling lens systematically has been studied. With the combination of the customizable DMD elements and alterable projective scaling system, 2D designable patterned microstructures with multi-scale size range from millimeter to hundred nanometer have been achieved by a single exposure. In addition, an engineered Fresnel zone plate (FZP) with numerical aperture (NA) of 0.36 and focal length of 114 μm has been achieved by a single exposure of 1.2 s. The acquisition of the array of FZP lens shows the stability and efficiency of the pattern process. The proposed method could be expected to play an important role in the flexible and efficient fabrication of engineered 2D multi-scale structures.