There are different approaches in philosophical justification of the influences of metaphysical or spiritual causes on the material world. According to the approaches of the the most Muslim thinkers, the deposited factors are influencing the on material world, but such influencing is along with the natural and material causes. Accordingly, is it possible to propose a methodological materialism in sciences that consider the experimental method in methodology of science to describe and explain the material world, despite of non-inclusivism of the existence in the material? This article is to prove the fact that, accepting the aforementioned principles, would not lead to a methodological materialism. Accordingly, neglecting the unseen world and inner world, and analyzing the material causes disregarding the spiritual causes would provide an incomplete knowledge for human.