Silkworm (Bombyx mori) pupae lipid profiles were analyzed using high-resolution mass spectrometry-based lipidomics. A total of 241 lipid molecular species were annotated with high confidence in male and female silkworm pupae. Triacylglycerol (TG), phosphoethanolamine (PE) and phosphocholine (PC) were the main lipid subclasses of silkworm pupae, accounting for 63, 41 and 38 lipid molecular species, respectively. No unique lipid molecular species were identified, but there were differences in the abundance of lipid molecular species between male and female silkworm pupae. Therefore, the differences in the lipid abundance of male and female silkworm pupae were analyzed by chemometrics. As a result, 8 lipid molecular species were screened for differential lipids. Hierarchical clustering analysis (HCA) showed that male and female silkworm pupae samples formed two distinct branches, indicating that these differential lipids could potentially be used as biomarkers to distinguish between male and female silkworm pupae.