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In order to explore the main regulatory genes and related pathways of growth traits, transcriptome sequencing was first performed on the brain, liver, and muscle tissues of 3-month-old <i>M. armatus</i> with different growth rates. By comparative transcriptome analysis of fast-growing and slow-growing groups of <i>M. armatus</i>, a total of 2887 DEGs were screened, of which 59 up-regulated genes and 105 down-regulated genes were detected in the brain, 146 up-regulated genes and 202 down-regulated genes were detected in the liver, and 529 up-regulated genes and 1846 down-regulated genes were detected in muscle, including insulin-like growth factor binding protein 1a (<i>IGFBP1A</i>), insulin-like growth factor binding protein 1b (<i>IGFBP1B</i>), myosin, light chain 1 (<i>MYL1</i>), and myoglobin (<i>MB</i>). Through Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, we identified a total of 288 significantly enriched GO entries and 68 significantly enriched KEGG pathways related to growth, such as skeletal muscle tissue development, insulin-like growth factor binding, and the mitotic cell cycle. These key genes and signaling pathways may play a key role in regulating the growth of <i>M. armatus</i>. Digging into the regulatory mechanisms of these key genes will provide a theoretical basis for further exploration of the molecular mechanisms related to the growth and development of <i>M. armatus</i>, and help to breed new varieties of <i>M. armatus</i> with rapid growth.