An early-maturity mutant KFJT-1 has been screened out after carbon ion irradiation in sweet sorghum (Sorghum bicolor (L.) Moench). In this study, tissue specific digital gene expression analysis was performed between the KFJT-1 mutant and the wild type KFJT-CK at seedling stage. The results showed that a total of 717, 2160 and 2,331 tags-mapped genes were differently expressed in roots, stems and leaves of young seedling, respectively. In KFJT-1, 557 (77.7%) genes were up-regulated and 160 (22.3%) genes were down-regulated in young root; 1,232 (57.0%) genes were up-regulated and 928 (43.0%) were down-regulated in young stem; and 1,577 (67.7%) genes were up-regulated and 754 (32.3%) genes were down-regulated in young leaf. Functional annotation revealed that most induced genes functioned as "binding", "synthase activity", "transferase" and "transporter activity" which involved in the biological processes of metabolic and response to stimulus. Surprisingly, the up-regulated genes in KFJT-1 were classified into four KEGG pathways: "alpha-Linolenic acid metabolism", "flavonoid biosynthesis", "inositol phosphate metabolism" and "fatty acid biosynthesis", which related to the stress resistance and supported the outstanding agronomic traits of KFJT-1 in the process of plant growth and development. Among the DEGs, a critical photoreceptor from photoperiod pathway PHYA gene was significantly up-regulated in leaf and root of KFJT-1, suggesting the mutation could occur on the genomic upstream of PHYA. This work may provide helpful insights to further understand the mutation mechanism in sweet sorghum.