Pyriproxyfen is a juvenile hormone-like pesticide. Once intake occurs, it leads to a series of poisoning characters consequences in silkworm, Bombyx mori (ID: 7091, Lepidoptera), such as non- cocooning, non-pupation, production of low-active eggs, and extended stages. However, the poisoning mechanism is still unclear. Here, silkworms were fed mulberry leaves soaked with different pyriproxyfen concentrations, and the heads were dissected for transcriptome analysis, while the hemolymph was used for determinations of ecdysone and juvenile hormone titers. As a result, after conjoint analysis of 3 feeding groups and a control group, 555 differentially expressed genes (DEGs) were obtained, which were mainly involved in hormone metabolism, glycometabolism and protein metabolism. Meanwhile, 119 genes were significantly correlated with the pyriproxyfen concentrations, and they were mainly involved in drug metabolism and glycometabolism. The ecdysone titers in several feeding groups were significantly lower than those of the control group, while juvenile hormone was not detected in all groups, including the control and feeding groups. Correspondingly, due to activation of the juvenile hormone signaling pathway by pyriproxyfen, key genes in the ecdysone synthesis pathway were downregulated, and a large number of downstream genes were up- or downregulated. In addition, nearly all genes in the detoxification pathway were upregulated. These results suggested that, affected by the juvenile hormone signaling pathway, ecdysone titers decreased and further affected a series of downstream processes, and this was the key reason for pyriproxyfen poisoning in silkworm, B. mori, which could lay a foundation for the study of pyriproxyfen resistance in silkworm.