20-Hydroxyecdysone (20E), the most important regulator for insect development, is also a major component in phytoecdysteroids in plants. Therefore, this plant-derived hormone is considered as a potential natural product for use in pest management. However, some insects show high resistance to it, and the molecular mechanism of their resistance is still unclear. In this study, we find that the cotton bollworm Helicoverpa armigera larvae show high tolerance to artificial foods containing up to 50 µg 20E without any detrimental effects on growth and development. High performance liquid chromatography analysis indicates that high efficiency to transform the ingested 20E through an ecdysteroid esterification pathway may contribute to the resistance. Furthermore, comparative transcriptome analysis of the larvae's midgut after 20E treatment identifies two genes (long-chain-fatty-acid-CoA ligase, Long-FACL; sterol O-acyltransferase, SATF) involved in the pathway. Transcriptome and real-time PCR show the Long-FACL gene can be significantly induced by 20E, and this induction is only detected in the midgut. However, 20E has no effect on the transcript of the SATF gene. Moreover, the heterologously expressed protein of the SATF gene shows the ecdysteroid-22-O-acyltransferase activity that requires fatty acyl-CoA, which is produced by Long-FACL. Taken together, our results identify and demonstrate the genes involved in the ecdysteroid esterification pathway conferring high resistance to 20E in the cotton bollworm, H. armigera.