The goal of this study was to understand the effect of light intensity on the chlorogenic acid content and biosynthesis-related gene expression in Marsdenia tenacissima. In this study, M. tenacissima plants were treated with different light intensities; the chlorogenic acid content was determined by high-performance liquid chromatography; and transcriptome sequencing was performed. The amount of chlorogenic acid in the control was the highest and differed significantly from that under three different shading treatments. With a decrease in light intensity, the content of chlorogenic acid also showed a decreasing trend. A total of 1149 differentially expressed genes were identified by transcriptome sequencing, and most of the genes were down-regulated under the 90% shading treatment. A weighted gene co-expression network analysis identified the differentially expressed genes associated with light-induced chlorogenic acid biosynthesis. The different shading treatments down-regulated the expression of the chlorogenic acid biosynthesis pathway structural genes (HCTs). The MIKC family genes were the main transcription factors regulating light-induced chlorogenic acid biosynthesis, but the MYB and SBP family genes were also involved. In summary, combined physiological and transcriptome analysis, candidate structural genes, and transcription factors in the biosynthesis pathway of chlorogenic acid were identified in M. tenacissima.