Identification of cotton and linen fabric is difficult in the qualitative analysis of textile fibers. Its request to testers is high and its test result is easy to be affected by artificial factors. Through comprehensive analysis of the mid-infrared spectra of cotton and linen and the crystallinity and orientation degree which reflect the crystal structures of cotton and linen by the methods of correlation analysis and peaks' intensity ratio, the characteristic spectra and reference spectra of cotton and linen are obtained. Because there is a significant difference between cotton and linen in orientation degree, the mid-infrared characteristic wavelength of orientation degree is selected. Then, through regression analysis, the regression equation for orientation degree and mid-infrared spectra of cotton and linen is obtained. The regression equation can be used to identify cotton and linen. The method is simple, convenient, nondestructive and environmental. A test person even without any textile knowledge can complete the test in 2 minutes less. The result shows that the method can simplify the identification of cotton and linen so as to improve operation efficiency.