Cycas panzhihuaensis, an endangered species distributed in the dry-hot valleys of southwestern China, faces drought (D), heat (H), and their combination (DH) under current and future climatic conditions. To explore the responses of C. panzhihuaensis to D, H, and DH, chlorophyll fluorescence and the lipid and fatty acid profiles were determined. Leaf water loss and leaf damage only occurred following DH treatment. The photochemical activity was least impacted by D stress and most severely impacted by DH stress. D treatment reduced the levels of most lipid categories and total fatty acids. Both the H and DH treatments led to a significant decrease in the levels of saccharolipids, lysophospholipids, sphingolipids, and fatty acyls, while significantly increasing the levels of neutral glycerolipids and fatty acids. Moreover, odd-numbered fatty acids and trans-fatty acids-C18:2ttn-6 accumulated significantly following both H and DH treatments. However, the levels of both total fatty acids and total lipids were significantly lower after DH stress compared to H stress. The proportion of saturated fatty acids increased after D treatment and that of polyunsaturated fatty acids increased after both H and DH treatments. Following various treatments, the degree of unsaturation in total phospholipids decreased, while that in total saccharolipids remained unchanged. Additionally, the unsaturation levels of diacylglycerol and triacylglycerol showed no change after D stress, but increased after H and DH treatments. In conclusion, C. panzhihuaensis exhibited varying levels of tolerance to D, H, and DH treatments, which may be related to the differential adjustments in lipid composition and unsaturation levels.