This research is based on two presuppositions: first is that disciplines of knowledge -including humanities- are organized and systematic and second is that we ought to seek for the impact of religion on science in the philosophy of science. Having adopted a descriptive-analytic method, this essay goes to study the relation between science and religion in the light of Allamah Misbah’s view and through a process-centered approach. The scheme of knowledge and its main constituents as a passive element stands on one side, and Allamah Misbah’s theological principles concerning the scope and aims of religion as an active element in man’s life stand on another. The study of the two sides leads to the conclusion that the subject matter of humanities -due to their close ties with the aims of religion and in the light of cognitive value of narrated propositions of religion- is to be revised. Any change in the subject-matter entails a modification in the structure of issues and propositions of humanities. The tie between subjectology and methodology and the perplexity of the subject-matter of humanities gave rise to the need of the scheme of humanities for revealed traditions along with none-revealed resources and their influence on it. Moreover, viewing the impact of religion on the goals of knowledge, normative propositions as a part of humanities come under influence, too.