Research Background: State Islamic Religious Universities (PTKIN) in Indonesia, especially State Islamic Universities (UIN), are required to bridge the progress of science and religious values in the midst of globalisation and technological development. UIN K.H. Abdurrahman Wahid Pekalongan responds to this through the philosophy of ‘Harmonisation of Science’ to harmonise science and religion in higher education. Methods: This study uses a library research and content analysis approach to analyse curriculum documents, performance reports, and lecturer publications to extract patterns of science-religion integration. Data validity was tested through source triangulation and peer debriefing. Key Findings: This study found that the Harmonisation of Science philosophy is translated through three main axes, namely academic excellence, humanism, and moderation, which are manifested in the curriculum, pedagogical practices, and research culture. The results of the analysis show the important role of religious moderation in scientific development at UIN. Contribution: This article contributes by offering a systematic analysis of the application of the philosophy of Harmonisation of Science, filling the void of literature that was previously only normative. It also develops an interdisciplinary analytical framework to evaluate institutional outcomes in the context of Islamic higher education. Conclusion: This research shows that the integration of science and religion at UIN K.H. Abdurrahman Wahid Pekalongan has been holistically implemented through three main scientific paradigms: UIN Unggul, UIN Humanis, and UIN Moderat, which combine Islamic values with contemporary science. Further studies are needed to explore the implementation of these paradigms in various faculties.