Phryma leptostachya is a well-known medicinal plant that produces furofuran lignans with various biological activities. However, the biosynthetic pathways of these natural products in P. leptostachya remain unclear. Hairy root cultures provide a novel method for elucidating the biosynthetic pathways of secondary metabolites. Here, we established a hairy root system for P. leptostachya by optimizing five parameters: Agrobacterium strains, explant types, infection time, A. rhizogenes cell density, and acetosyringone (AS) concentration. The highest transformation frequency (74.51 %) was achieved when the stem explants were infected with ATCC15834 (OD600 = 0.8) strain of A. rhizogenes for 30 min on 1/2 MS medium supplemented with 200 µM AS. Based on the optimal protocol, RNAi hairy roots were induced by silencing the cytochrome P450 gene, PlCYP81Q38, which converts (+)-pinoresinol to (+)-sesamin by means of (+)-piperitol in P. leptostachya, to determine its in vivo role in the lignan biosynthetic pathway and verify the availability of this system. PlCYP81Q38 silencing resulted in significant down-regulation of the PlCYP81Q38 gene at the transcriptional level, consistent with a remarkable decrease in the content of leptostachyol acetate and 6-desmethoxy-leptostachyol acetate, demonstrating its significance in the production of lignans. In conclusion, the approaches and results presented here provide a solid foundation for elucidating the role of key genes involved in the lignan biosynthesis pathway in P. leptostachya and for the industrial production of lignan through plant biotechnology.