A double-sided maskless exposure system and method consists of light sources which includes two light wavelength segments, maskless optical engines in which a 2D spatial light modulation (spatial light modulator) device, such as DMD, is generating a plurality of pixel array of the pattern, vision system, moving substrate and computer control system. The double-sided maskless exposure system at least includes two maskless optical engines with auto-calibration function which can correct any alignment error in-line. Each optical engine is for each side of the substrate. The optical engines are aligned each other in pairs and are simultaneously patterning on each side of the moving substrate. The system also includes a manipulator for moving, stepping or scanning the optical engines, relative to the substrate so that it can create a contiguous whole image on the both sides of the subject.