The invention discloses a deep processing method of tobacco stem shreds. The deep processing method comprises the following steps: firstly, rewetting stem shreds with large size defects; then, mixingthe rewetted stem shreds and tobacco leaves according to a preset weight ratio; then, shredding the mixed stem shreds and tobacco leaves to obtain initially-shaped stem shreds; finally, sequentially shredding the initially-shaped stem shreds. According to the deep processing method, the stem shreds with large size defects are rewetted and mixed with the tobacco leaves and the mixed stem shreds andtobacco leaves are shredded, so that due to presence of the tobacco leaves, an interaction force between the stem shreds can be greatly reduced, and the shape of the stems can be greatly reduced, andthus the situation of powdering of the stem shreds can be greatly reduced; meanwhile, the stem shreds with large size defects are shredded once, so that the sizes of the stem shreds can become smaller and thinner and can be closer to the shredded tobacco size of a thin cigarette, namely the problem that a cigarette making machine and the quality of the produced thin cigarette are easily affectedby the still large sizes of the tobacco stem shreds after processing is avoided.