The invention provides a control method of a shredded tobacco winnowing system, which comprises the steps of acquiring current weight m1 of first screenings at a screenings outlet of a primary winnowing machine, comparing m1 with preset weight m0 of the first screenings at the screenings outlet of the primary winnowing machine, and adjusting fan frequency of a secondary winnowing machine accordingto a comparison result of m1 and m0. The method can achieve quick adjustment and precise control of a sliver removal rate at a shredded tobacco winnowing outlet and a shredded tobacco content in removed slivers, and therefore improves purity of finished shredded tobaccos.