Beyond Reductionism is the aim of complexity theories in methodology.However, some great confusion arises in many relevant discussions on reductionism.This article carefully distinguishes two basic shapes of the reductionism from broader and deeper view: ontological reductionism belief and reduction method in methodology.The article stresses that transcendence of reductionism in ontology and reduction in methodology are non-isomorphic problems of different levels.Epistemological analysis of reductionism shows that the separating nature of human thinking is the origin of reductionism thinking,and that a weak reduction is necessary for all sciences.