Although interdisciplinary research has garnered extensive attention in academia, its core knowledge structure has yet to be systematically explored. To address this gap, this study aims to uncover the underlying core knowledge topics within interdisciplinary research, enabling researchers to gain a deeper understanding of the knowledge framework, improve research efficiency, and offer insights for future inquiries. Based on the Web of Science (WoS) database, this study collected 153 highly cited papers and employed the LDA topic model to identify latent topics and extract the knowledge structure within interdisciplinary research. The findings indicate that the core knowledge topics of interdisciplinary research can be categorized into four major areas: the knowledge framework and social impact of interdisciplinary research, multidisciplinary approaches in cancer treatment and patient care, Covid-19 multidisciplinary care and rehabilitation, and multidisciplinary AI and optimization in industrial applications. Moreover, the study reveals that AI-related interdisciplinary research topics are rapidly emerging. Through an in-depth analysis of these topics, the study discusses potential future directions for interdisciplinary research, including the cultivation and development of interdisciplinary talent, evaluation systems and policy support for interdisciplinary research, international cooperation and interdisciplinary globalization, and AI and interdisciplinary research optimization. This study not only uncovers the core knowledge structure of interdisciplinary research but also demonstrates the effectiveness of the LDA topic model as a data mining tool for revealing key topics and trends, providing practical tools for future research. However, this study has two main limitations: the time lag of highly cited papers and the dynamic evolution of interdisciplinary research. Future research should address these limitations to further enhance the understanding of interdisciplinary research.