In Metaphysical Foundations of Natural Science, Kant tries to prepare a pure part for Newtonian physics to show it is a proper science. Meanwhile, he purges Newtonian physics from the concepts which are empty or are not justified from the stand point of critical philosophy and puts concepts consistent with this philosophy in their place. In some crucial positions, therefore, he diffess from Newton and one of them is the constitution of matter. Although Newton belives in atomism, Kant presents his dynamical theory of matter according to which matter essentially has fundamental forces on which its possibility is based. Kant criticizes atomism from the standpoint of transcendental philosophy and considers his theory consistent with this philosophical view. In this essay, these two rival theories are is examined to understand Kant’s motivation in presenting his novel theory.