The invention provides a processing technology for lowering pectin content in a cut stem, which comprises the following steps of: A) sieving and peeling: cutting a thick stem into even stem sections of 8-10mm, sieving according to the thickness, enabling the thick stem section of which a diameter is less than 2.38mm to directly enter the next working procedure, peeling and polishing the thick stem of which a diameter is more than or equal to 2.38mm, and removing the bast part of a tobacco stem by mechanical force; B) chemical stem cleaning and dipping: after the tobacco stem is cleaned with sodium metaphosphate contained citric acid solution of which the pH (potential of hydrogen) is 3.0+/-0.5, keeping the temperature of 50-60DEG C, and dipping for half hour; C) washing the stem with clean water; D) after feeding, pressing and cutting off the stem; and E) drying and storing the stem. Compared with the cut stem prepared by the traditional technology, the cut stem prepared with the method disclosed by the invention has the advantages that the physical behavior does not have obvious difference, but the aesthetic quality is obviously improved, the irritation is reduced, and the miscellaneous qi is reduced. After the cut stem is added into rolled cigarettes, the cigarette sucking comfort can be improved, and the tar content is lowered.