The invention discloses a laser flexible micro-processing system and method based on a liquid crystal spatial light modulator. The system comprises a laser, a first reflecting mirror, a half-wave plate, a beam expander, a second reflecting mirror, a first spatial light modulator, a second spatial light modulator, a quarter-wave plate, a first lens, a third reflecting mirror, a spatial filter, a fourth reflecting mirror, a second lens, a beam splitter, a third lens, a CCD camera, a galvanometer, a field lens, a working table and a computer. With the utilization of the wavefront modulation characteristic of the liquid crystal spatial light modulator, a widely adaptable flexible laser processing technology which is controllable in multiple parameters such as laser beam quantity, beam shape and quality, polarization state and angular momentum is provided; in conjunction with wavefront measurement and feedback technology, not only can wave front aberration be corrected, but also a high-energy beam can be decomposed into random two-dimensional or three-dimensional low-energy multiple beams, and parameters of the beams such as shape and polarization state can be flexibly controlled, so that the laser processing technology has the advantages of high quality, high efficiency, extremely high adaptability and flexibility.