From the deep structure of the history of scientific thought, this paper discusses the classical Needham puzzle, that is, why the modern scientific revolution did not take place in China. Focusing on the foundation period of the European scientific revolution in the 17th century, this paper proves that the birth of modern science has profound metaphysical particularity by comparing the fundamental division between Chinese and Western philosophy of physics (or natural philosophy). The paper holds that the breakthroughs of modern science in Europe are rooted in a unique set of philosophical presuppositions: A “mechanistic cosmological view” that is mathematical, composed of particles of matter, and follows the universal external law established by God. This world picture encourages abstraction, quantification, experimental decomposition and causal reduction of nature. In contrast, China’s mainstream natural philosophy is a kind of “organic cosmological view,” which regards the universe as a life network composed of “Qi” and ganying, and its exploration mode tends to grasp relevance, mode, and dynamic balance, rather than to find universal and linear causality. This paper concludes that the fundamental differences between the two world views in ontology, epistemology, and methodology lead to different evolutionary paths of the knowledge system between China and the West. Modern science is not the inevitable product of universal rationality, but the fruit of the special philosophy of “mechanics.”