The Cry1Ab/Cry1Ac transgenic crops can effectively control pests. In the present study, the world-wide distribute pest, Indian meal moth Plodia interpunctella (Hübener), was taken as the research object. The genes closely related to Bt toxin protein were sequenced using a high-throughput sequencing to reveal the insecticidal mechanism of Bt transgenic rice. The results showed that the de novo assembly generated a total of 37,246 unigenes among of which 23,310 unigenes could be annotated after the transcriptome sequencing was performed on the non stressed population and Bt transgenic rice meal stressed population of Indian rice borer, respectively. Then, 34,466 significantly differentially expressed genes including 15,741 up-regulated genes and 18,725 down-regulated genes were determined by the Reads Per kb per Million reads (RPKM) method. Our database provides powerful tools for transcriptome analysis of P. interpunctella and further understanding of the molecular basis of Bt related mechanisms in P. interpunctella.