<p>Coral bleaching, driven by rising ocean temperatures, disrupts the symbiosis between corals and their photosynthetic symbionts (dinoflagellates of the family Symbiodiniaceae). This review summarizes current knowledge of lipidomic adaptations and dysfunctions during thermal stress with focus on the pivotal role of lipids in corals’ resilience and in the bleaching process. Susceptibility to bleaching varies depending on the morphology, symbiont species, and lipid reserves of corals. Under heat stress, symbionts undergo thylakoid membrane remodeling, which alters their glycolipid and phospholipid composition, and thermosensitive symbionts are also experience oxidative damage. In the host coral, immune responses involve sphingolipid and phosphatidylinositol signaling, oxylipin-mediated inflammatory pathways, and oxidized phospholipids that mark necrotic tissues. Lipid remodeling, including changes in glycerophospholipid, sphingolipid, and betaine lipid profiles, provides membrane stability and metabolic adaptation. Neutral lipids serve as energy reserves but are depleted under long-term stress exposure, impairing recovery. In view of accelerated climate change, understanding lipid-mediated stress responses is essential for predicting coral survival and developing targeted interventions. Future research should integrate multi-omics approaches to elucidation of coral–symbiont metabolic interactions and development of lipid-based strategies that would help enhance reef resilience in the warming ocean.</p>