The butterflies are one of the insect groups which undergo typical complete metamorphosis in their life history. However, up to now, little is known about the genomic mechanism that regulates the butterfly metamorphosis. In this study, using a swallowtail butterfly P. polytes as a model organism, a high-throughput sequencing platform was employed to perform the transcriptome and gene expression analyses in order to explore the P. polytes transcriptome features during different developmental stages. The results showed that approximately 398 million useful (Q20) reads were assembled into groups of 14698 (L1), 14264 (L2), 15084 (L3), 15520 (P1), 15052 (P2), 15720 (P3) and 15709 (A1), 14668 (A2), 16152 (A3) genes, respectively, with 58.19% to 67.11% of the data successfully mapped to the reference genome; the transcriptome change analysis via the DEGs Package revealed that dramatic gene expression differences were presented among the different developmental stages, that is, totally, 1162, 891 and 1723 genes were differentially expressed between adult and pupal, adult and larval, larval and pupal stages, respectively, with a number of these differentially expressed genes associated with the functions of digestion, cuticularization, chemoreception, wing formation, and so on. These differentially expressed genes and potential candidate genes required for butterfly metamorphosis by comparative transcriptomics may shed some new insights on molecular mechanisms underlying complete metamorphosis.