Spotted stem borer, Chilo partellus, undergoes larval diapause (hibernation and aestivation), and depends on the food reserve accumulated during feeding stage for its survival. Lipids are the primary source of energy during diapause, and essential for different cellular, biochemical and physiological functions. However, there is no information on lipid and lipophilic compound contents during different stages of hibernation, aestivation and nondiapause in C. partellus. Thus, we compared the concentration and composition of lipids in pre-diapause, diapause and post-diapause stages of hibernation and aestivation with nondiapause stages of C. partellus. The studies revealed significant differences in total lipids and various lipophilic compounds during different stages of diapause as compared to nondiapause C. partellus. The total lipids were significantly lower during diapause stage of aestivation and hibernation as compared to nondiapause larvae. Further, the linoleic acid, Methyl 3-methoxytetradecanoate, and l-(+)-Ascorbic acid 2,6-dihexadecanoate were significantly lower, and oleic and palmitoleic acids greater during pre-diapause and diapause stages of hibernation and aestivation as compared to nondiapause larvae. The cholesterol content was significantly greater during pre-diapause stage of hibernation, and diapause and post-diapause stages of aestivation as compared to nondiapause stages. The unsaturation ratio was significantly higher in the pre-diapause and diapause stages and lower in post-diapause stage of aestivation than the hibernation and nondiapause states. This study provides insights on differential lipid profiles during different phases of diapause, which could be useful for further understanding biochemical and physiological cross-talk, and develop target-specific technologies for the management of C. partellus.