It was during its “Christian Century” (1549–1650) that Japan first encountered Western natural philosophy via the Jesuit missionaries. This paper explores how and why these missionaries emphasized cosmology in their evangelical activities. My central argument is that the Jesuits considered cosmological knowledge a very effective “spiritual weapon” in the first stage of their conversion plan in Japan: 1) to convince the initiates on the superiority of Christianity over local religions by demonstrating the existence of God on a logical and rational ground, then 2) to instill more strictly Christian doctrines, and finally 3) to reach Baptism. Many textual evidences show that cosmological ideas were closely tied to the references to “divine design,” which are found in treatises on catechism. This was the distinctive character of the early Jesuit mission in Japan.