The frequency and intensity of the occurrence of drought (D) events during winter are increasing in most areas of China. To explore the interactive effects of D and freezing temperature (F) on plants of endangered Cycas panzhihuaensis, some physiochemical characteristics and the lipid profile were determined. Drought and F stress had no or little impact on the traits of leaves, which, however, bleached following a combination of D and F treatment (DF). Drought treatment did not affect the chlorophyll fluorescence parameters and the flavonoid content of C. panzhihuaensis. Besides the increase in flavonoid content, a decrease of photochemical efficiency and an increase of heat dissipation were induced by both F and DF treatment, with the effects being greater in the latter treatment. The malondialdehyde content decreased significantly and the total antioxidant capacity increased significantly in the plants exposed to both D and DF treatments. The D treatment did not impact the amount of phospholipids but led to an accumulation of saccharolipids. Additionally, the amount of both phospholipids and saccharolipids remained unchanged following F treatment but decreased significantly following DF treatment compared with those of the control. The unsaturation level did not change significantly in most lipid classes of membrane glycerolipids following various stresses but increased significantly in phosphatidylserine, monogalactosylmonoacylglycerol, digalactosyldiacylglycerol and sulphoquinovosyldiacylglycerol following D or both D and F treatments. Generally, plants of C. panzhihuaensis showed relatively strong tolerance to individual D stress, while D aggravated the F-induced damage, which was likely caused by the degradation of the membrane glycerolipids.