To reduce the stem sliver content in cut tobacco of slim cigarettes and the cut tobacco content in online removed stem sliver, improve cut tobacco size distribution, and enhance product quality and its stability of slim cigarettes, a three-stage flexible pneumatic separation system was designed adapting to high-flow pneumatic separation of cut lamina of slim cigarettes based on the two-stage pneumatic separation system of cut lamina. The system was mainly made up of input unit, loosening roller, three-stage pneumatic separation tanks, cyclone blanker (settling blanker), transportation unit, output unit, dust extraction pipe and other parts. Its first and second stage pneumatic separation system could screen stem sliver out from cut tobacco at the largest degree, and the third stage pneumatic separation system screened cut tobacco out from removed stem sliver, realizing the effective decrease of the stem sliver content in cut tobacco and increasing recycle of cut tobacco in removed stem sliver. A brand of slim cigarette of Huanghelou was test on the new pneumatic separation system, and the results showed that it could decrease the stem sliver content in cut tobacco and the cut tobacco content in removed stem sliver effectively. The rate of cut tobacco content in removed stem sliver decreased by more than 20%, and the rate of stem sliver content in cigarettes was reduced from 1.06% to 0.74%. The physical indicators of cigarettes have been improved to varying degrees, and the appearance quality defects such as puncture of cigarettes have been effectively ameliorated. The system improved the product quality and the comprehensive utilization rate of raw materials at the same time, and provided a technological support for sustainable and healthy development of slim cigarettes.