Background: Sarcandra glabra is an evergreen and traditional Chinese herb with anti-oxidant, anti-bacterial, anti-inflammatory, and anti-tumor effects. Recently, artificial light-emitting diodes (LEDs) have been widely used as energy for plants in greenhouse. However, little is known regarding the effects of the different LED lights on plant growth and the regulatory mechanism of phenylpropanoid-derived compounds accumulation patterns in S. glabra. Results: Compared to white LED light (WL), the red LED light (RL) significantly increased the plant height and decreased the stem diameter and leaf area, whereas blue LED light (BL) significantly suppressed the height and leaf area of S. glabra. According to the results of transcriptomic profiling, 861, 378, 47, 10,033, 7917, and 6379 differentially expressed genes (DEGs) were identified among the groups of leaf tissue under BL (BY) vs leaf tissue under RL (RY), BY vs leaf tissue under WL (WY), RY vs WY, root tissue under WL (WG) vs WY, stem tissue under WL (WJ) vs WG, and WJ vs WY, respectively. We identified 46 unigenes encoding for almost all known enzymes involved in phenylpropanoid biosynthesis, e.g., phenylalanine ammonia lyase (PAL), 4-coumaroyl CoA ligase (4CL), chalcone synthase (CHS), flavanone 3-hydroxylase (F3H), and flavonol synthase (FLS). We found 53 unigenes encoding R2R3-MYB proteins and bHLH proteins, respectively, where several were related to flavonoids biosynthesis. Based on metabolomic profiling, a total of 454 metabolites were identified, of which 44, 87, and 296 compounds were differentially produced in WY vs RY, WY vs BY, and WY vs WG, respectively. In BY, the production of esculetin, caffeic acid, isofraxidin, and fraxidin were significantly reduced, while the yields of quercitrin and kaempferol were significantly up-regulated. In RY, the contents of cryptochlorogenic acid, cinnamic acid, and kaempferol were significantly decreased. In addition, the production of metabolites (e.g., chlorogenic acid, cryptochlorogenic acid, and scopolin) were significantly reduced, whereas the yields of metabolites (e.g., esculetin, fraxetin, isofraxidin, and fraxidin) were significantly promoted in WG. Conclusion: These results provide further insight into the regulatory mechanism of phenylpropanoid-derived compounds accumulation patterns in S. glabra under different light conditions, enabling the development of optimum breeding conditions for this plant.