Sugarcane (Saccharum officinarum L.) is very important crop for sugar and energy production worldwide with highly economic-value, growing in tropical and subtropical regions. However, abiotic stresses including chilly adversely affect its growth and productivity. With growing the consideration of nanotechnology in reduction the adverse effects of environmental stresses in plants, the present study investigates the transcriptome responses of graphene nanoparticles (GrNPs) in sugarcane (Guitang 49 cultivar) under chilly stress. The treatments were set as control, chilling (4ºC), GrNPs [50 part per million (ppm)] and chilling + GrNPs. Samples were collected and subjected to physiological determination and transcriptome analyses. Chilly treatment induced an increase in rate of membrane leakage and malondialdehyde (MDA) content. The combined applications of Chillying + GrNPs ameliorated the oxidative damage. RNA-Seq-based transcriptome analysis followed by the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis pointed out that the mainly enriched KEGG pathways that were detected in almost all treated combinations are: plant hormones signal transduction, phenylpropanoid biosynthesis, starch and sucrose metabolism, carotenoid biosynthesis and photosynthesis antenna proteins. The detected up and downregulated DEGS involved in these pathways could be useful to understand the mechanisms underlying the response to graphene.