The involvement of UIN Sunan Kalijaga Yogyakarta in the integration of scientific discourse, led to the development of distinctively scientific paradigm, namely integration-interconnection. A decade running, the university has developed a new academic tradition, characterized by patterns of development in the field of research and the products of scientific work of the academic community. This article reveal the scientific development as shown in the work of the lecturers. With the perspective of philosophy of science, this study sees theimplementationof UINSunanKalijagaYogyakartaparadigmonthelevel of science development pattern. Therefore the object of the study is the books of lecturers through critical survey methods, a model of research by reading, understanding the purpose, comparing and identifying certain aspects in the frame of the reader. In general, the works of the lecturers is to strengthen, develop, and detailing the scientific paradigm, which he developed. However, there are some works which is the application of the four models of the application of scientific development, namely complementation, confirmations, contributions, and comparisons. This pattern turns placing al-Quran and al-Sunnah in a position parallel with the concepts, theories, and scientific findings, while in the paradigm building of “spider web”, both sources plays as “central of science”