The formation of modern human sciences which are presently taught at the academic centers of the world dates back to the modern period in the West; an era which is known as the period of the separation of science, religion, intellect, and faith from each other. The theoretical principles of this field of knowledge are limited to matter from an ontological standpoint, to anthropology from a humanist standpoint, to secularism from an eschatological standpoint, and to sense perception, experience, verification, and instrumental intellect from an epistemological standpoint. The question is what the contexts and background of the formation of modern human sciences in the West are, and what epistemological, religious, psychological, and spiritual harms they might lead to. Following a descriptive-analytic design and through a historical review of the problem of knowledge in the West, the present study intends to revisit the epistemological factors influencing the formation of the human sciences of the modern period and their disadvantages. Restricting science to scientism; human being to humanism; the world of being to natural phenomena; acquisition of knowledge to sense perception, empiricism, causality, and pure rationalism, as well as focusing on an epistemological distinction between phenomena and things in-themselves, and ignoring inner sense and fitri (intrinsic) knowledge, intuitive intellect and revelation are among the significant factors which play roles in the formation of modern western human sciences. Moreover, they underlie the creation of epistemological, religious, and psychological crises; spiritual poverty; nihilism, and the like in the world today.