The invention discloses a paraffin sectioning method for Corydalis saxicola Bunting stems. The paraffin sectioning method comprises the following steps: sample fixation, dehydration, transparency treatment, wax dipping, embedding, sectioning and slice expansion, dewaxing, dyeing and slice sealing. The paraffin sectioning method specifically comprises the following steps: before the transparency treatment, putting dehydrated Corydalis saxicola Bunting stems into a 0.8%-1.2% sarranine solution, and carrying out dip dyeing for 8-12 hours; after the dewaxing, carrying out rehydration on a slide carrying the Corydalis saxicola Bunting stems, putting the Corydalis saxicola Bunting stems into an alcohol solution, carrying out color separation, simultaneously adding acetic acid into the alcohol solution for the color separation in a volume ratio of 1 to (800-1000), finally, putting the Corydalis saxicola Bunting stems into a 0.8%-1.2% fast green solution, and carrying out dyeing for 10-20 seconds. By virtue of the paraffin sectioning method disclosed by the invention, a clear Corydalis saxicola Bunting stem structure can be sectioned, a specimen can be stored for a long time for use, is a permanent microscopic slide specimen and can be applied to microscopic identification of Corydalis saxicola Bunting medicinal materials for market normalization.