The damages by three mildews namely Aspergillus niger, Aspergillus terreus, and Chaetomium globosum, commonly found in mildew-caused paper deterioration, on the properties of wood-free paper were investigated in this study. X-ray fluorescence spectroscopy and X-ray diffraction analysis were employed to examine the changes of element and crystallinity of paper after the mildew test. The X-ray fluorescence analysis showed that the contents of phosphorus and sulfur of wood-free printed paper significantly increased with the period of the mildew test. Results from X-ray diffraction analysis also confirmed that all three mildews degraded the crystallinity of paper. A. niger caused the greatest damage on the cellulose crystalline region of paper after the mildew test.