Seed germination is triphasic in nature. Phase I is characterized by rapid water imbibition that plateaus during Phase II. Phase III is defined by second upturn in imbibition as the radicle protrudes from seed and starts elongating. During phase I, cell membranes of seed undergo reorganization from a leaky hexagonal II to a stable lamellar configuration to avoid the cytoplasmic leakage. Low temperature decreases membrane flexibility resulting in the disruption of membrane reorganization, substantial cytoplasmic leakage and thus seed metabolic dysfunction. Cold acclimating genotypes tend to remodel their membrane fluidity by changing the composition of membrane lipids. Adjustment of membrane fluidity maintains an environment suitable for the successful completion of germination process. Keeping this in view, we comparatively profiled changes in membrane lipids after 3(phase I) and 6 hours(phase II) of imbibition under normal(30°C) and low temperatures(12°C) in cold-tolerant(FA205-1) and sensitive(SA0582) cotton seeds. Results showed that sphingolipids abruptly increased only in FA205-1 seeds in response to cold stress. Sphingolipids undergo significant interactions with cholesterol which can maintain fluidity and biophysical order of the cell membranes. Phosphatidylcholine(PC) is another important lamellar-forming membrane lipid which observed to increase only in FA205-1 seeds. The oxidation of choline head group of PC produces ammonium compounds like Gly-betaine which serves as an osmo-protectant in cell. The fatty acid(FA) unsaturation of phosphatidylglycerol(PG) directly determines the flexibility of plastid membranes and thus embryo survival. The unsaturation proportions of the PG molecules were observed to be higher in FA205-1 seeds after 3 hours of imbibition under cold stress. In addition, changes in unsaturation/saturation ratios were also compared for each of the phospholipid class and it was observed to be higher in FA205-1 seeds compared to SA0582 seeds. The unsaturated FAs prevent close packing of lipids resulting in the maintenance of membrane flexibility even under cold stress.