Temperature influences microbial physiology and metabolism, which is influential to their industrial applications. The strategies for adaptive response to temperature are still unclear in oleaginous fungus Cunninghamella echinulata. This study aimed to understand the mechanism of lipid metabolism of C. echinnuiata responds to long-term temperature changes by coupling lipidomics and transcriptomics. Compared with 25 C and 15 C, lipid content of C. echinnulata was the highest at 35 C, with the following lipid strategies: genes associated with lipogenesis were upregulated, increasing the precusors and NADPH supply, and pyruvate-oxaloacetate-malate cycle was significantly activated to produce NADPH; the increase of PC/PE ratio and PI content decreased membrane rigidity and enhanced its fluidity, upgrading fatty acid turnover and secretion. Ribosome metabolism was also significantly enhanced to restrain protein synthesis and prefer lipid synthesis. This work comprehensively explained the dynamics of lipid and transcriptomic profile in C. echinnulata responding to temperature, providing an insight into the future development of lipid-related cell factories.