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Prior knowledge is one of the strongest predictors of academic performance. Yet, research on its relationship with academic emotion remains limited. This study aims to address this gap from a profile-based perspective that considers the co-occurrence of multiple academic emotions. Importantly, inspired by the advancement of emotion psychology, academic emotion profiles are characterized at the individual level. Academic emotion profiles are found to be more heterogeneous for students with lower prior knowledge; EEG analyses also revealed neural representations that differentiated levels of prior knowledge. Based on behavioral and neural evidence, our study advances the understanding of how prior knowledge influences academic emotions and highlights the importance of personalized emotional support for students with lower prior knowledge.