[Objectives]  To analyze the roles of differentially expressed genes and metabolic pathways related to lipid metabolism in the diapause of Exorista civilis. [Methods]  High-throughput sequencing was used to complete the transcriptomic analysis of diapausing and non-diapausing pupae. Differentially expressed genes related to lipid metabolism were screened with bioinformatic methods and analyzed using GO and KEGG enrichment. [Results]  GO enrichment analysis indicates that differentially expressed genes were enriched to 48 GO terms and that the largest number were enriched by biological processes. KEGG enrichment analysis successfully annotated 112 differentially expressed genes involved in 15 pathways, of which 48 were up-regulated and 64 down-regulated. Differentially expressed genes were mainly involved in the glycerophospholipid metabolism, fatty acid degradation and the glycerolipid metabolism. Differentially expressed genes enriched in these pathways showed different expression trends. [Conclusion]  Fatty acyl-CoA reductase, stearoyl-CoA desaturase (delta-9 desaturase), and glycerol-3-phosphate dehydrogenase are differentially expressed in the lipid metabolism of E. civilis, and may therefore play an important role in formation of the epidermis, cold resistance and energy transfer, during diapause.