Lasioderma serricorne is an important pest in the storage of tobacco and grains. s-methoprene is among the most widely used juvenile hormone analogues (JHA). However, the molecular mechanism of s-methoprene on Lasioderma serricorne was not clear. Thus, the survival number, pupation rate, mortality rate, and transcriptome of L. serricorne larvae (Larvae of L. serricorne exposed to s-methoprene at 0.0, 0.5, 5.0, and 50.0 × 10−5 mg/cm2 for 2 weeks were referred to as LS0, LS0.5, LS5, and LS50, respectively) exposed to different doses of s-methoprene were studied. After 2 weeks of exposure to s-methoprene, there were significant differences in the number of larvae and pupation rate between the treatment and control groups. By analyzing the gene expression patterns and whole transcriptome of L. serricorne larvae, a total of 468, 4003 and 5132 differentially expressed genes (DEGs) were identified (LS0.5 vs LS0, LS5 vs LS0, and LS50 vs LS0, respectively). A total of 120 commonly up-regulated genes and 3659 commonly down-regulated genes were identified in LS5 vs LS0, and LS50 vs LS0. Weighted gene correlation expression network analysis (WGCNA) identified five modules comprising all transcripts, with the blue module closely related to the LS50. Moreover, the genes of the blue module were highly correlated with “biological processes (1162 genes)”, “cellular components (1507 genes)”, and “molecular functions (1446 genes)”. Three transcription factor genes TRINITY_DN3652_c0_g1_i12, TRINITY_DN6508_c0_g2_i1 and TRINITY_DN184_c0_g2_i2 were identified as hub genes in the blue module. The expression changes of these genes indicated that the expression levels of non-biological related genes, such as enzymes, protein metabolism, and signal transduction may change under s-methoprene stress. The present results revealed the molecular mechanism of the adaptability of L. serricorne to s-methoprene stress, providing a reference for further exploring the molecular mechanism of s-methoprene on L. serricorne.