Based on self-determination theory and achievement goal theory, this study provided a serial multiple mediation model that examined how students’ perceptions of teacher autonomy support (PTAS) relate to different achievement motivations (mastery and performance-approach goals), and further associate with students’ intellectual risk-taking (IRT) engagement and academic performance (AP). A self-report questionnaire and a standardised science academic test were completed by 520 primary school students from China. The structural equation modelling revealed that the positive association between PTAS and students’ AP was serially mediated by achievement motivations and then intellectual risk-taking engagement. Though the unexpected negative direct effects of PTAS on AP suggested the need to optimise autonomous instructional practices, the positive indirect and total effects highlighted the contributions of PTAS to students’ achievement motivation and IRT engagement. The findings instantiated how autonomy support may promote students’ achievement motivations and further influence their learning engagement and academic performance in science. This study would be valuable for educational researchers and practicing teachers as it extends our understanding of what factors are influential in promoting students’ learning outcomes and how they correlate in science learning processes.