Sugarcane is a major cash crops cultivated in tropical and subtropical regions around the globe. This crop is mainly considered cold sensitive, although some cultivars showed resistance to cold stress. The crops respond to cold stress in diverse mechanisms and among these mechanisms, genes expression is one of the significant biological pathways. Our goal was to study the involvement of gene expression in cell organelles and cognate targets in the tolerance to low temperatures in sugarcane. The results reported here indicated that 2,324 genes were found upregulated in cultivar GT08-1108 organelles in a total of 5,649 upregulated genes, while 1,252 genes were found downregulated in a total of 3,289 downregulated genes. Furthermore, the cultivar ROC22 gene expression analysis showed that a total of 2,223 genes were found upregulated in 5,558 total upregulated genes, while 1,449 genes were found downregulated in a total of 3,252 downregulated genes. The gene expression analysis in both cultivars showed that during cold stress, the gene expression in the vacuole was found significantly downregulated. Hence, from these findings, we concluded that during cold stress, the most affected organelle is the vacuole. Collectively, our findings suggested that cold stress seriously affected cellular organelles in sugarcane. Hence, more research is needed to identify more cold tolerant cultivars using transcriptomics approaches in sugarcane, which could be significant for better production and quality of sugarcane.