The quality of planting materials is the foundation for productivity, longevity, and berry quality of perennial grapevines with a long lifespan. Manipulating the nursery light spectrum may speed up the production of healthy and high-quality planting vines but the underlying mechanisms remain elusive. Herein, the effects of different monochromatic lights (green, blue, and red) on grapevine growth, leaf photosynthesis, whole-plant carbon allocation, and transcriptome reprograming were investigated with white light as control. Results showed that blue and red lights were favorable for plantlet growth in comparison with white light. Blue light repressed excessive growth, significantly increased the maximum net photosynthetic rate (Pn) of leaves by 39.58% and leaf specific weight by 38.29%. Red light increased the dry weight of the stem by 53.60%, the starch content of the leaf by 53.63%, and the sucrose content of the stem by 230%. Green light reduced all photosynthetic indexes of the grape plantlet. Photosynthetic photon flux density (PPFD)/Ci-Pn curves indicated that blue light affected photosynthetic rate depending on the light intensity and CO concentration. RNA-seq analysis of different organs (leaf, stem, and root) revealed a systematic transcriptome remodeling and (CONSTITUTIVELY PHOTOMORPHOGENIC 1), (ELONGATED HYPOCOTYL5), (HY5 HOMOLOG, (early light-induced protein) and (PHYTOCHROME INTERACTING FACTOR 3) may play important roles in this shoot-to-root signaling. Furthermore, the correlation network between differential expression genes and physiological traits indicated that (photosystem II subunit S), (photosystem II subunit 28), , (sucrose synthase 4), and (fructose-bisphosphate aldolase) were pertinent candidate genes in responses to different light qualities. Our results provide a foundation for optimizing the light recipe of grape plantlets and strengthen the understanding of light signaling and carbon metabolism under different monochromatic lights.