Cyperus esculentus is unique in that it can accumulate rich oil in its tubers. However, the underlying mechanism of tuber oil biosynthesis is still unclear. Our transcriptional analyses of the pathways from pyruvate production up to triacylglycerol (TAG) accumulation in tubers revealed many distinct species-specific lipid expression patterns from oil seeds and fruits, indicating that in C. esculentus tuber: (i) carbon flux from sucrose toward plastid pyruvate could be produced mostly through the cytosolic glycolytic pathway; (ii) acetyl-CoA synthetase might be an important contributor to acetyl-CoA formation for plastid fatty acid biosynthesis; (iii) the expression pattern for stearoyl-ACP desaturase was associated with high oleic acid composition; (iv) it was most likely that endoplasmic reticulum (ER)-associated acyl-CoA synthetase played a significant role in the export of fatty acids between the plastid and ER; (v) lipid phosphate phosphatase (LPP)-δ was most probably related to the formation of the diacylglycerol (DAG) pool in the Kennedy pathway; and (vi) diacylglyceroltransacylase 2 (DGAT2) and phospholipid:diacylglycerolacyltransferase 1 (PDAT1) might play crucial roles in tuber oil biosynthesis. In contrast to oil-rich fruits, there existed many oleosins, caleosins and steroleosins with very high transcripts in tubers. Surprisingly, only a single ortholog of WRINKLED1 (WRI1)-like transcription factor was identified and it was poorly expressed during tuber development. Our study not only provides insights into lipid metabolism in tuber tissues, but also broadens our understanding of TAG synthesis in oil plants. Such knowledge is of significance in exploiting this oil-rich species and manipulating other non-seed tissues to enhance storage oil production.