In this study, Macleaya cordata were stressed by PEG6000 simulating drought and mechanical damaging, and HPLC was used to detect the contents of protopine, allocryptopine, sanguinarine and chelerythrine. It was found that the contents of end products in Macleaya root such as sanguinarine and chelerythrine increased by 30% PEG6000 sximulating drought stressing and mechanical damaging. On the contrary, the contents of intermediate products such as protopine and allocryptopine reduced. Meanwhile, there was up-regulation in expression of synthetic genes DBOX and P6H in sanguinarine and chelerythrine. After RT-PCR was used to detect related gene expression, the expression of synthetic genes DBOX and P6H in sanguinarine and chelerythrine were up-regulated. The appropriate drought stress and mechanical damage might be advantageous to sanguinarine and chelerythrine accumulation in root of Macleaya, which provided the theoretical basis for Macleaya planting in arid and desertification areas and combining livestock feeding and Macleaya planting.