This study is to investigate John Calvin``s view of the natural science in his commentaries of the Bible, dealing with themes such as his Aristotelian cosmology, his attitude of Copernican theory, and his understanding of the creation story and the flood story in the Bible. Though Calvin believed the traditional cosmology represented by Aristoteles and never accepted the new astronomy of Copernican theory, he did not condemn Copernicus and his followers unlike Luther and Melanchton. He was positive about the development of the natural science, because he thought it would reveal the hidden secret and providence of God the Creator. He argued the Scripture should not be considered as a source of scientific information, but as the book of furnishing knowledge of Jesus Christ, which used the very common language and style for uneducated people. It meant that the Bible could not be compatible with his contemporary scientific knowledge. Accordingly, he developed and applied the principle of accommodation to interpret the creation story and the flood story in his biblical commentary. His theory of biblical interpretation made scientists free from biblical literalism and develop the natural science.