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In response to mixed findings on the impact of inquiry-based learning (IBL) on students’ science career expectations (SCE), this study proposed a comprehensive framework grounded in Identity-Based Motivation theory to examine relationships among inquiry-based learning, achievement motivation, science identity, and science career expectations. A sample of 371 tenth-grade students from a national-level high school in Jiangsu, China, were surveyed using validated instruments. Structural equation modeling revealed that IBL did not directly affect SCE; however, science identity mediated this relationship. Furthermore, IBL indirectly affected SCE through the chain mediation of achievement motivation and science identity. These findings provided valuable insights for educators seeking to enhance students’ SCE and underscored the importance of IBL in shaping the next generation of science-related professionals.