The invention relates to an optical fiber cladding processing method, in particular to a method and system for processing superfine single crystal optical fiber cladding. In order to solve the problems of complex process route, low efficiency, poor repeatability, poor precision and the like of the existing method for preparing the single crystal optical fiber cladding, the method comprises the following steps of: simulating to obtain the diameter and the depth of a microstructure; determining the theoretical focusing spot diameter of an optical system; shaping a laser beam into a Bessel beam;carrying out space cutting on the Bessel beam; determining a microstructure manufacturing focal depth h; segmenting an optical fiber; and adjusting the focal length, and processing the microstructureon the surface of the optical fiber; The system comprises a laser, and a zoom beam expander, a variable annular diaphragm, a spatial light modulator, a reflector and a focusing microscope objective which are sequentially arranged in an emergent light path of the laser, and further comprises a laser ranging\automatic focusing device. According to the method and system, the optical fiber is segmented, each segment corresponds to different focal lengths, the processing of each segment of the optical fiber is realized by adjusting the focal lengths on line, and the processing precision is high.