Allium mongolicum Regel is a valuable desert plant, yet its functional genomic research is hindered by low genetic transformation efficiency due to monocot regeneration recalcitrance and dense tissue structures. This study established a dual genetic transformation platform for A. mongolicum, encompassing in vivo transient expression and stable hairy root induction. By evaluating various infiltration methods, vacuum impregnation was identified as the optimal transient strategy and was successfully applied to localize the candidate proteins AmJAZ2 and AmSWEET14 to the nucleus and plasma membrane, respectively. For stable transformation, shortened stems were utilized as the optimal target explants. An orthogonal experimental design was employed to optimize key parameters, including Agrobacterium density, acetosyringone concentration, vacuum parameters, and co-cultivation duration. GFP fluorescence and PCR analysis confirmed the stable integration and expression of the transgene in the induced hairy roots. In conclusion, this study establishes preliminary, species-specific genetic transformation protocols for A. mongolicum, providing a baseline technical reference that may support subsequent exploratory research on the molecular biology and secondary metabolism of this species.