The poor utilization of carbohydrate in commercial cultured fish species remains an unsolved biological question in aquaculture sector. Now days, advancement in the molecular biology along with progress in next generation sequencing technology provides way forward to understand molecular level investigation at genome wide-scale in any organisms. Hence, the present study intended to investigate molecular events or pathways during inclusion of high carbohydrate diet in the commercially important farmed Jayanti rohu carp, Labeo rohita, which is first genetically improved farmed carp in the Indian subcontinent. In order to reveal, global transcriptional changes in the liver of Jayanti rohu fingerlings, 45 days feeding experiment were conducted in the cemented tanks of fingerlings fed with 20% (Control), 40% and 60 % gelatinized starch diet. Through transcriptome sequencing by Illumina HiSeq500, a total of 25.99 million illumina pair-end reads were generated from pooled libraries, assembled, average 88.35% quality reads were aligned and successfully mapped to reference database using HISAT algorithm. The DESeq was used for comparative expression profiling among control and treated fishes with 40% and 60% carbohydrate regime resulted in total 15232, 15360 differentially expressed genes (DEGs) (P < 0.05), including 4464, 4478 up-regulated genes and 4343, 4171 down regulated genes, respectively. Those identified DEGs represented in different metabolic pathways such as Glycolysis/Gluconeogenesis, Insulin signalling pathway, Carbohydrate metabolism, FoxO signaling pathway, etc. The transcripts associated with glycogen synthesis such as hexokinase, glycogen synthase, PHK and PGK were found up-regulated in liver of fishes fed with high CHO as compared to control, indicated enrichment of glycogenesis mechanism in the liver. In addition to this, up-regulation of transcripts such as ACCα, PPARγ and FAS in liver of fishes fed with high CHO indicated enrichment of de novo lipogenesis. The functional enrichment analysis using Gene Ontology (GO) term of transcripts highlighted different activities and enriched 3113, 2465 & 775 GO terms associated with biological function, molecular function and cellular component, respectively. Further, KEGG pathway analysis showed that of Insulin signalling pathways, PPAR and mTOR pathway significantly enriched or induced due to inclusion of high CHO level in the fishes compared to control groups. The six selected differential expressed transcripts were validated using qPCR and shown consistent results with generated the liver transcriptome data. Overall our study first time revealed the presence of an atypical regulation or activations of several regulatory genes/enzymes of glycolysis, glycogenesis and de novo lipogensis in the liver of rohu carp due to incorporation of high carbohydrate in the regime. Our result provides a clue/assist to undertake genetic selection program based on screening of glucose tolerance level of each rohu family at molecular level. This study also provides lead to undertake early nutritional programming in rohu fishes, which in turn able to adapt the assimilation of high carbohydrate diet.