Glycerolipids are the principal constituent of cellular membranes; remodelling of glycerolipids plays important roles in temperature adaptation in plants. Temperate plants can endure freezing stress, but even chilling at above-zero temperatures can induce death in tropical species. However, little is known about the differences in glycerolipid response to low temperatures between chilling-sensitive and freezing-tolerant plants. Using ESI-MS/MS-based lipidomic analysis, we compared the glycerolipidome of chilling (4 and 10 °C)-treated rice with that of freezing (-6 and -12 °C)-treated Arabidopsis, both immediately after these low-temperature treatments and after a subsequent recovery culture period. Arabidopsis is a 16:3 plant that harbours both eukaryotic and prokaryotic-type lipid synthesis pathways, while rice is an 18:3 plant that harbours only the eukaryotic lipid synthesis pathway. Arabidopsis contains higher levels of galactolipids than rice and has a higher double bond index (DBI). Arabidopsis contains lower levels of high melting point phosphatidylglycerol (PG) molecules and has a lower average acyl chain length (ACL). Marked phospholipid degradation occurred during the recovery culture period of non-lethal chilling treated rice, but did not occur in non-lethal freezing treated Arabidopsis. Glycerolipids with larger head groups were synthesized more in Arabidopsis than in rice at sub-lethal low-temperatures. Levels of phosphatidic acid (PA) and phosphatidylinositol (PI) rose in both plants after low-temperature treatment. The DBI and ACL of total lipids did not change during low-temperature treatment. A higher DBI and a lower ACL could make the membranes of Arabidopsis more fluid at low temperatures. The ability to synthesize glycerolipids containing a larger head group may correlate with low-temperature tolerance. The low-temperature-induced increase of PA may play a dual role in plant responses to low temperatures: as a lipid signal that initiates tolerance responses, and as a structural molecule that, on extensive in large accumulation, could damage the integrity of membranes. Changes in ACL and DBI are responses of plants to long-term low temperature.