During the late sixteenth and early seventeenth centuries, Jesuit missionaries in China published a variety of apologetic and polemical materials in literary Chinese. In these, they opposed the Neo-Confucian idea of cosmogony as the natural evolution of a primordial substance called qi, following set patterns called “principle” or li, with their own Aristotelian-Thomistic interpretation of the process of creation. This article will first summarize the Neo-Confucian view, and then present the Jesuit view as taught in their colleges by looking at their normative commentary on the subject as discussed by Aristotle. Following that, it will examine the cases made by two Jesuits, Matteo Ricci and Giulio Aleni, in books published in China. Lastly it will explore two specific philosophical issues upon which the two sides failed to connect by looking at the unarticulated presuppositions that impeded communication: (1) the issue of the infinite regress, and (2) the nature of causality itself.