Cotton is the most important natural fiber crop in the world. Cotton fiber cells are not only the major economic product of cotton, but also an ideal material for studying the growth and development of plant cell. The fiber cell elongation and secondary cell wall development of short and thick fiber mutant ligon lintless-1 (li-1) are severely impaired. However, its mechanism is still unclear. Boosting evidence showed that sphingolipids and sterols play important roles in the growth and development of fiber cell. But it is unknown that the changes of these lipids are in the li-1 fiber cells. In the study, we detected the lipid profiles of 10-DPA and 20-DPA fiber cells of wild type (TM-1), and 10-DPA fiber cells of li-1 mutant by untargeted and targeted lipidomics. In the result, seven lipid classes, 33 lipid sub-classes, and 793 lipid molecular species were detected by untargeted lipidomics. Nine sphingolipid species and seven sterols were detected by targeted lipidomics. The PA, PC, PE, PI, CER, CerG1, DG, TG, and AGlcSiE enriched in fiber cells. 23 lipid sub-classes and 82 lipid molecular species were altered significantly between 10-DPA and 20-DPA fiber cells. Compared with 10-DPA fibers, the lipid intensity of 16 sub-classes and 56 lipid molecular species decreased while 7 lipid sub-classes and 26 lipid molecular species increased in the fibers at stage of SCW deposition (20-DPA). Similarly, obvious difference was detected between li-1 and TM-1 fibers. Compared with TM-1, 20 lipid sub-classes and 60 lipid molecular species increased significantly, only five lipid sub-classes and eight lipid molecular species decreased in li-1 mutant. It is surprising that the sitosterol ester increased by 59.56 fold in li-1 fibers. Detailed sphingolipid and sterol profiles indicated all molecular species of S1P, PhytoCer-OHFA, and GluCer increased while all molecular species of Sph, PhytoSph, and GIPC decreased in li-1 fibers. The mutant fiber cells showed a significantly increase in campesteryl ester, sitosteryl ester, and total steryl ester, with 21.8, 48.7, and 45.5 fold increases, respectively. Moreover, transcriptome analysis indicated that the different expression genes between TM-1 and li-1 fibers enriched in the pathway of fatty acid elongation and degradation, glycosphingolipid biosynthesis, glycerophospholipid metabolism, and brassinosteroid biosynthesis. Furthermore, the number of oil body also increased in li-1 leaf and fiber cell when compared with wild type. These results illuminated that fiber cell elongation was blocked in the li-1 mutant was not due to a lack of lipids, but rather lipid over-accumulation (obesity), which may result from the disruption of sphingolipid and sterol metabolism. This study provides a new perspective for further studying the regulatory mechanisms of fiber development.