The invention discloses a method and system for processing cut stems for fine cigarettes. After tobacco stems are subjected to primary slicing, feeding, swelling, drying and winnowing, the stem slices are subjected to secondary slicing, and the width of the cut stems obtained after secondary slicing is 0.8-1.2 mm; aiming at the fine cigarettes, secondary slicing is adopted, proper cut stem forms are effectively obtained, the obtained cut stems are low in wood smell, wet, fine, smooth and permeable in smoke, free of pungent stimulation and burning heat sensation, smooth in throat entering, clean and comfortable in remaining taste and good in universality and compatibility, meanwhile, the whole cut rate of the cut stems is effectively guaranteed, and the breakage rate is reduced. The whole system and method take the two purposes into consideration, and high practicality is achieved. According to the processing system, all equipment can be independently arranged or connected through conveying equipment, and conveying efficiency is effectively improved.