Artemisinin, isolated from Artemisia annua L., is recommended as the preferred drug to fight malaria. Previous research showed that JA mediated promotion of artemisinin accumulation was dependent on light. However, the mechanism underlying the interaction of light and JA in the regulation of artemisinin accumulation is still unknown. We identified a WRKY transcription factor, AaWRKY9, using transcriptome analysis. The glandular trichome-specific AaWRKY9 positively regulates artemisinin biosynthesis by directly binding to the promoters of AaDBR2 and AaGSW1. The key regulator in the light pathway AaHY5 activates the expression of AaWRKY9 by binding to its promoter. In addition, AaWRKY9 interacts with AaJAZ9, a repressor in the JA signaling pathway. AaJAZ9 represses the transcriptional activation activity of AaWRKY9 in the absence of methyl jasmonate. Notably, in the presence of MeJA, the transcriptional activation activity of AaWRKY9 is increased. Taken together, our results reveal a novel molecular mechanism underlying AaWRKY9 contributes to light- and jasmonate-mediated to regulate the biosynthesis of artemisinin in A. annua. Our study provides new insights into the integration of the two signaling pathways to regulate terpene biosynthesis in plant.