Cycas panzhihuaensis inhabits regions where summer temperatures can exceed 40 °C, and these extreme conditions may intensify with ongoing global warming. However, how this species adapts to such thermal extremes is not well understood. To investigate the responses of C. panzhihuaensis to heat stress, some physiological characteristics along with lipid and fatty acid profiles were analyzed. The results show that heat stress induced soil water loss but did not cause leaf water loss and visible symptoms of leaf damage. However, photoinhibition was induced and heat dissipation was inhibited under the stress. In the recovered plants, both heat dissipation and maximum photochemical efficiency exhibited significant increases compared to the stressed plants but did not return to the control level. Most lipid categories including phospholipids and saccharolipids accumulated significantly following both the stress and subsequent recovery. However, the content of total neutral glycerolipids maintained unchanged after various treatments. The ratio of phosphatidylcholine/phosphatidylethanolamine decreased significantly and the ratios of both digalactosyldiacylglycerol/monogalactosyldiacylglycerol and triacylglycerol/diacylglycerol increased significantly in the stressed plants. Compared to the control plants, the relative content of polyunsaturated fatty acids significantly increased, while that of both saturated and monounsaturated fatty acids significantly declined in both stressed and recovered plants. Under stress conditions, the unsaturation levels of total neutral glycerolipids and their constituent components significantly increased, whereas those of phosphatidylglycerol and total saccharolipids exhibited a marked decrease. In conclusion, C. panzhihuaensis can tolerate extremely high temperatures to some extent which might be associated with the adjustments in lipid composition and unsaturation levels.