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This study examines gender differences in the effects of interdisciplinary research (IDR) on academic career outcomes, emphasizing IDR as a subversion strategy to challenge male-dominant disciplinary paradigms. IDR, by breaking knowledge boundaries and integrating methods from diverse fields, offers female researchers an opportunity to carve out niches in a competitive and gender-imbalanced academic environment. Using theoretical frameworks from the sociology of knowledge, feminist theory, and boundary work, this study hypothesizes that female PhD students are more likely to engage in IDR as an intellectual strategy and that their career outcomes are influenced by structural inequalities in academia. Employing a novel semantic measure of interdisciplinarity and linking novel mentorship dataset with publication datasets, the study explores the intersectionality of gender and IDR in shaping academic trajectories. The findings aim to contribute to the understanding of how IDR serves as both a pathway for innovation and a strategy for navigating systemic academic inequalities.