The previous publication identified that pyruvate dehydrogenase E1 () positively regulated the process of male reproduction in through affecting the expressions of insulin-like androgenic gland hormone. The present study aimed to identify the potential male-reproduction-related genes that were regulated by through performing the transcriptome profiling analysis in the testis and androgenic gland after the knockdown of the expressions of by the injection of . Both RNA-Seq and qPCR analysis identified the significant decreases in expressions in the testis and androgenic gland in injected prawns compared to those in -injected prawns, indicating the efficiency of in the present study. Transcriptome profiling analysis identified 56 and 127 differentially expressed genes (DEGs) in the testis and androgenic gland, respectively. KEGG analysis revealed that the energy-metabolism-related pathways represented the main enriched metabolic pathways of DEGs in both the testis and androgenic gland, including pyruvate metabolism, the Citrate cycle (TCA cycle), Glycolysis/Gluconeogenesis, and the Glucagon signaling pathway. Thus, it is predicted that these metabolic pathways and the DEGs from these metabolic pathways regulated by may be involved in the regulation of male reproduction in . Furthermore, four genes were found to be differentially expressed in both the testis and androgenic gland, of which ribosomal protein S3 was down-regulated and uncharacterized protein LOC113829596 was up-regulated in both the testis and androgenic gland in -injected prawns. The present study provided valuable evidence for the establishment of an artificial technique to regulate the process of male reproduction in .