The high damage rate of mechanical cutting and low harvesting efficiency of stem mustard is a major constraint to the sustainable development of its industry. In this study, a reciprocating cutter device tailored for stem mustard was designed for stem mustard under special growing conditions in southwest China. A reciprocating cutter model was developed based on ANSYS/LS-DYNA. Parameters considered include cutting height (X₁), angle of incision (X₂), forward speed (X₃) and single run displacement (X₄). Cutting force (F) and cutting power (P) were identified as evaluation metrics. A multifactor quadratic regression model was developed for the orthogonal combinatorial testing procedure using the Box–Behnken design methodology. Cutting force and cutting power obtained by applied derivation of regression equations were 41.4 N and 36.756 W, respectively. Response surface methodology and analysis of variance (ANOVA) were used to determine the optimum operating parameters of the cutting tools used for machining, which were determined to be X₁ = 1.45 mm, X₂ = 12°, X₃ = 0.5 m/s and X₄ = 93 mm. The maximum cutting success rate of 94% and the minimum damage rate of 6% on stemmed mustard under the optimum combination of cutting parameters were verified through several field trials. The results of this study provide valuable technical insights into the optimal design of harvesting equipment for stem and leaf mustard to improve the success rate and reduce the damage rate.