Lotus (Nelumbo nucifera Gaertn.) contains various bioactive compounds, with benzylisoquinoline alkaloids (BIAs) as one of the major groups. The biosynthetic pathways of two major bioactive BIAs in this plant, nuciferine and N-nornuciferine, are still not clear. Therefore, several genes related to BIA biosynthesis were searched from the lotus database to study the role of key genes in regulating these pathways. In this study, the expression profiles of NCS, CNMT, 6OMT, CYP80G2, and WRKY TFs were investigated in mechanically wounded lotus leaves. It was found that the accumulation of nuciferine and N-nornuciferine significantly increased in the mechanically wounded lotus leaves in accordance with the relative expression of putative CYP80G2 and one WRKY transcription factor (NNU_24385), with the coregulation of CNMT. Furthermore, the role of methyltransferase-related genes in this study suggested that methylation of the isoquinoline nucleus to yield a methylated-BIA structure may occur at the N position before the O position. Altogether, this study provides improved understanding of the genes regulating BIA biosynthesis under stressed conditions, which could lead to improvements in BIA production from the commercial lotus.