The idea of reconstruction of Islamic philosophy in modern conditions is actualized due to the fact that there are problems of a natural and social nature, which can be designated as catastrophes and crises. In such critical conditions of challenge, a synthesis of spirituality and scientificity is in demand, which is the foundation for solving emerging difficulties and consolidating humanity. In this regard, the authors of the article turn to the widely discussed controversy in modern Islamic discourse on the compatibility of Islam and science and come to the conclusion that it is inevitable to support and expand the possibilities of rational research and the search for knowledge inspired by the Qur’an. A classic historical example of the rationalization of knowledge in Islamic discourse is the Arabic-Greek philosophy - falsafa (al-falsafa al-’arabiyya al-mu’aṣira). The complex problems of the current level of development of religion, science, politics, economics, culture, and civilization require new research approaches, new dimensions and tools in the XXI century. The theory of self-organization and evolution of large nonlinear systems has become a new fact and factor in the development of the science of studying complex local and global problems.