Low non-freezing temperature is one of the major environmental factors that affect metabolism, growth, development and geographical distribution of chilling-sensitive plants, Jatropha curcas, a chilling-sensitive plant, which is considered as a sustainable energy plant with great potential for biodiesel production. Our previous studies showed that short-term chilling shock at 5 °C for 4 h and long-term chill hardening at 12 °C 1 or 2 days could improve chilling tolerance of J. curcas seedlings, but lipidomic response to chilling shock and chill hardening has not been elucidated. In this study, membrane lipid composition change in J. curcas seedlings during chilling shock and chill hardening was investigated by liquid chromatography-electrospray ionization-mass spectrometry (LC–ESI–MS) approach. The results indicated that the relative abundances of nine classes and 72 species of membrane lipids, such as phosphatidylethanolamine (PE), phosphatidylcholine (PC), phosphatidylglycerol (PG), phosphatidylinositol (PI), lysophosphatidylcholine (lysoPC) and lysophosphatidylglycerol (lysoPG), two glycolipids digalactosyldiacylglycerol (DGDG) and monogalactosyldiacylglycerol (MGDG) and a sulfoquinovosyldiacylglycerol (SQDG), were significantly changed, and the degree of unsaturation of above-mentioned cellular membrane lipids with fatty acid differing in chain lengths and the number of double bonds also increased in varying degrees during chilling shock and chill hardening. These results suggested that remodeling and increase in the degree of unsaturation of membranes lipids may be a common physiological basis for short-term chilling shock- and long-term chill hardening-induced chilling tolerance of J. curcas seedlings.