The onion thrips, Thrips tabaci (Thysanoptera: Thripidae), is a worldwide pest that causes serious damage to Allium crop species and acts as a vector for iris yellow spot virus (IYSV). In a previous study, we established an emamectin benzoate (EB) resistant strain (EB-R) with a 490-fold higher resistance ratio than the susceptible strain (SUS). The EB-R exhibited significantly increased transcript levels of glycine receptor alpha, glutamate-gated chloride channel (GluCl) b, and cytochrome P450 (CYP450) 6EB2 compared to SUS. To identify EB resistance-related genes that are differentially expressed genes between SUS and EB-R, we established an isogenic backcrossing strain and conducted transcriptome analysis after the 4th cycle of isogenic backcrossing. Among the 85 up-regulated genes in the transcriptome data, six cuticular protein genes showed up-regulation. Additionally, CYP450 4g15, which catalyzes the synthesis of cuticular hydrocarbons, exhibited a 6 log2-fold higher expression level in EB-R compared to SUS. Therefore, the elevated expression of genes associated with cuticle protein modification may be significantly is involved in the development of EB resistance.