Philosophy is the main question of science, whenever we would rather investigate a subject from the point of view of philosophy the generals and main questions about it would be asked by wisdoms’ minds. Although today philosophy has been considering as an independent science in all of the world natural sciences have been originating from natural philosophy. Chemistry is one of the natural sciences in which the perusing of the elements, atoms, molecules, and other chemical structures in addition to their behavior in the reactions and their features are done by it. Unfortunately, chemistry had had some dark sides in history and it has been ignoring by other majors insofar as some of the scholars preferable is to don't consider chemistry or its philosophy as an independent science. Do not consider chemistry and its philosophy autonomously has been forcing chemists to write and publish valuable books, articles, and discoveries what they are about chemistry and its philosophy ontology and methodology.