Tuber is a unique and extremely important organ of Cyperus esculentus, which is rich in oil and has the reproduction ability similar to seed. It is of great significance to study the specific expression genes in the tubers of Cyperus esculentus for analyzing the regulation mechanism of tuber-specific growth and development (especially oil accumulation). Through transcriptome sequencing of the main organs (root, leaf, tillering node, stolon and tuber) of Cyperus esculentus, the genes specifically expressed in tubers were comprehensively screened and the functions of related genes were analyzed. The results showed that a total of 155 tuber-specific expression genes were identified after multiple sets of comparative analysis by taking root, leaf, tillering node and stolon as reference, respectively. GO enrichment analysis showed that 7 GO terms including seed development, seed oilbody biogenesis, oil storage, abscisic acid response, response to heat, response to abiotic stimulus and protein folding were significantly enriched, and some of the genes involved in these GO terms just reflected the unique development characteristics similar to seed of Cyperus esculentus tubers. Among them, CESC_00080 and CESC_16572 encode caleosin, and meanwhile, CESC_08636, CESC_12549 and CESC_17828 encode oleosin, all of which are involved in the formation of plant oil bodies. Since oil body formation is a key step for plants to complete oil storage, it is indicated that the specific expression of these oil body formation-related genes in tubers may be the key to the storage of large amounts of oil in the tubers of Cyperus esculentus. In addition, this study also screened eight tuber-specific expression transcription factor genes, such as CESC_00448 (Abscisic acid insensitive 5-like protein ABI5) and CESC_03736 (Heat stress transcription factor C), some of whose potential target genes were found in identified tuber-specific expression genes, indicating that these transcription factor genes may regulate the specific expression of their respective target genes. In summary, the results of this study can provide an important reference for the construction of gene regulatory networks related to tuber development of Cyperus esculentus and the molecular mechanism analysis of tuber-specific gene expression.