One of the things that is neglected in the discourse on the Islamization of Contemporary Knowledge (ICK) is translating it into systematic methods in research or scientific development activities. In the context of natural science, which is the focus of this research, Syed Muhammad Naquib al-Attas, is a philosopher, not a scientist who works in a typical intellectual climate, for example conducting research in a laboratory or formulating theorems mathematically. Therefore, so that al-Attas' philosophical ideas can work more operationally and touch the methodological area, al-Attas' IOK must be brought into the realm of philosophy of science. In this study, the figure chosen in the philosophy of science discourse is Imre Lakatos. Lakatos was chosen because he is a scientist as well as an expert in the philosophy of science. In this writing, the research focuses on two things: (1) formulating the methodology of Islamic scientific research programs based on the conceptual framework of al-Atttas' Islamization of contemporary knowledge and Lakatos methodology of scientific research program; (2) reading the structure of the natural sciences and their problems, based on the formulation in point (1) as a starting point for re-conceptualizing, re-defining and re-formulating the key concepts of natural science. With a qualitative approach, the authors collect data from primary and secondary sources, then through descriptive, analytical and critical methods, the authors examine the data to arrive at the purpose of writing this thesis. Based on the analysis conducted, this research resulted in two things. First, the main structure of natural science, based on the framework of al-Attas and Lakatos, has four problems: (1) the problem of naturalism in worldview or hard-core, (2) the problem of realism in the paradigm, (3) the problem of reducing positivism in the formulation of theories and methodologies, (4) the problem of empirical correspondence theory of truth in conceptualization. These four problems ontologically based on the underlying metaphysical belief, namely naturalism necessarily modern science negates the metaphysical character that refers to issues of divinity and non-empirical matters. Second, to answer the four previous problems, Islamic natural science therefore needs to restore its metaphysical character with the following structure: (1) theism as a worldview, (2) metaphysical realism as a paradigm, (3) pluralistic affirmation of sources and frameworks for formulating theories and methodologies, (4) the truth of revelation as a limitation in conceptualization. The results of this study are expected to be one of the contributions in the discourse of IOK and Islamic science in general and the development of Islamic natural sciences in particular. Through this research, the author hopes to contribute to the major project of the Islamic Science Research Program, which is a scientific work that seeks to reformulate the concept of contemporary science as a long-term research program based on the Islamic worldview, as well as open a new discourse in the Islamic Natural Science Research Program in particular, a program long-term research based on the Islamic worldview in the fields of natural sciences such as physics, biology, chemistry, cosmology and their derivatives.