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The previous publication identified that pyruvate dehydrogenase E1 (<i>PDHE1</i>) positively regulated the process of male reproduction in <i>M. nipponense</i> 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 <i>PDHE1</i> through performing the transcriptome profiling analysis in the testis and androgenic gland after the knockdown of the expressions of <i>PDHE1</i> by the injection of <i>dsPDHE1</i>. Both RNA-Seq and qPCR analysis identified the significant decreases in <i>PDHE1</i> expressions in the testis and androgenic gland in <i>dsPDHE1-</i>injected prawns compared to those in <i>dsGFP</i>-injected prawns, indicating the efficiency of <i>dsPDHE1</i> 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 <i>PDHE1</i> may be involved in the regulation of male reproduction in <i>M. nipponense</i>. 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 <i>dsPDHE1</i>-injected prawns. The present study provided valuable evidence for the establishment of an artificial technique to regulate the process of male reproduction in <i>M. nipponense</i>.