Background <p>The red claw crayfish (<i>Cherax quadricarinatus</i>) is a commercially and ecologically significant species that displays a unique intersex model with an ovotestis gonad and was identified to have functional testes and a vestigial ovary, which was inhibited by insulin-like androgenic gland hormone (<i>IAG</i>), but the underlying molecular mechanisms are still unclear.</p> Results <p>In this study, the structure and transcriptomic profiles of ovotestis and female and male gonad was analysis and compared, 406 differentially expressed genes were identified, among which membrane-anchored AG-specific factor (<i>MAG</i>) exhibited significantly greater expression in ovotestis gonads than in male or female gonads. The localization of MAG in type I or II cells of androgenic gland revealed its potential function of IAG hormone synthesis. Furthermore, the analyses of gene regulation relationship revealed that <i>IAG</i> positively regulates <i>MAG</i> expression, while <i>MAG</i> negatively regulates vitellogenin gene (<i>VTG</i>) expression.</p> Conclusions <p>Our research suggesting <i>MAG</i> participates in the <i>IAG</i> regulated ovarian suppression in the intersex red claw crayfish, which provides important information on the regulatory mechanism of the ovarian dysplasia in the ovotestis of intersex red claw crayfish. These results will enhance the knowledge of <i>IAG</i>-related pathways in the female reproductive axis, as well as the mechanisms of sexual differentiation in crustaceans.</p>